Rationale: This script performs differential gene expression (dge) and calculates the upregulated and downregulated genes in lichen samples versus Xanthoria culture samples using edgeR and Sleuth
counts<-read.delim2("../analysis_and_temp_files/06_meta_mapping/kallisto_mycobiont_only.txt",sep=" ")
metadata<-read.csv2("../analysis_and_temp_files/06_meta_mapping/metadata_shared_with_neha.csv",sep=",")
# Extract locus_tag from target_id (XANPAGTX0501 for nuclear genome and GTX0501mito for mito genome) - OPTIONAL
counts[c("locus_tag","rest")]<-str_split_fixed(counts$target_id,'_',n=2)
# Tabulate the counts
counts_tab<-pivot_wider(counts[c(1,4,6)],names_from=sample,values_from = est_counts)
head(counts_tab)
## # A tibble: 6 × 32
## target_id XBC2 XBA1 XSA2_2 XSC1 XSE2 XBE1 XTA2 XSC2 XSA2 XBA2 XBC1
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 XANPAGTX05… 270 535 593.5 248 335.5 288 484 324.5 429.5 408 324.5
## 2 XANPAGTX05… 194 131 284.5 112 171.5 132 257.5 144 179.5 187 81
## 3 XANPAGTX05… 191.5 305 264.5 152.5 288 367 332 246.5 187.5 140 367
## 4 XANPAGTX05… 126 43.5 119.5 60.5 40.5 34.5 87.5 45 73 258.5 43.5
## 5 XANPAGTX05… 38 223 221 91 38 20 267 98 179 196 32
## 6 XANPAGTX05… 205 431 487 176 180 86 332 271 320 356 114
## # ℹ 20 more variables: XTA1 <chr>, XSA1 <chr>, MP_I <chr>, XTC2 <chr>,
## # XTE2 <chr>, XBE2 <chr>, XMC2 <chr>, MP_II <chr>, S_21XB1 <chr>,
## # KS21XB1 <chr>, S_21XB3 <chr>, S_42XB1 <chr>, S_42XB2 <chr>, S_42XB3 <chr>,
## # KS48XB1 <chr>, KS48XB2 <chr>, KS48XB3 <chr>, KS9XB1 <chr>, KS9XB2 <chr>,
## # KS9XB3 <chr>
write.table(counts_tab,"../analysis_and_temp_files/08_dge_culture_lichen/counts_table.tsv",quote=F,sep="\t",row.names = F) # Final table that will be used for dge calculation
full<-read.delim("../analysis_and_temp_files/08_dge_culture_lichen/counts_table.tsv",row.names=1)
d<-full %>% select(-MP_I,-MP_II) #remove MP_I and MP_II samples (based on previous correlation heatmaps)
colnames(d)
## [1] "XBC2" "XBA1" "XSA2_2" "XSC1" "XSE2" "XBE1" "XTA2"
## [8] "XSC2" "XSA2" "XBA2" "XBC1" "XTA1" "XSA1" "XTC2"
## [15] "XTE2" "XBE2" "XMC2" "S_21XB1" "KS21XB1" "S_21XB3" "S_42XB1"
## [22] "S_42XB2" "S_42XB3" "KS48XB1" "KS48XB2" "KS48XB3" "KS9XB1" "KS9XB2"
## [29] "KS9XB3"
head(d,5:5)
## XBC2 XBA1 XSA2_2 XSC1 XSE2 XBE1 XTA2 XSC2 XSA2
## XANPAGTX0501_000001-T1 270.0 535.0 593.5 248.0 335.5 288.0 484.0 324.5 429.5
## XANPAGTX0501_000002-T1 194.0 131.0 284.5 112.0 171.5 132.0 257.5 144.0 179.5
## XANPAGTX0501_000003-T1 191.5 305.0 264.5 152.5 288.0 367.0 332.0 246.5 187.5
## XANPAGTX0501_000004-T1 126.0 43.5 119.5 60.5 40.5 34.5 87.5 45.0 73.0
## XANPAGTX0501_000005-T1 38.0 223.0 221.0 91.0 38.0 20.0 267.0 98.0 179.0
## XBA2 XBC1 XTA1 XSA1 XTC2 XTE2 XBE2 XMC2 S_21XB1
## XANPAGTX0501_000001-T1 408.0 324.5 467.5 262 364.5 292.5 164.5 353.0 700.0
## XANPAGTX0501_000002-T1 187.0 81.0 178.5 163 199.0 183.0 99.0 113.0 66.5
## XANPAGTX0501_000003-T1 140.0 367.0 414.5 134 366.5 319.0 164.5 364.5 151.5
## XANPAGTX0501_000004-T1 258.5 43.5 59.5 74 53.0 29.5 47.0 27.5 11.0
## XANPAGTX0501_000005-T1 196.0 32.0 390.0 196 122.0 100.0 13.0 41.0 22.0
## KS21XB1 S_21XB3 S_42XB1 S_42XB2 S_42XB3 KS48XB1 KS48XB2
## XANPAGTX0501_000001-T1 302.5 716.0 452.5 333.0 356.5 454.5 462.5
## XANPAGTX0501_000002-T1 121.5 48.5 126.5 67.0 73.0 221.0 176.5
## XANPAGTX0501_000003-T1 216.0 142.0 206.5 202.5 217.5 197.5 214.0
## XANPAGTX0501_000004-T1 212.0 43.5 68.5 97.5 79.5 43.5 45.5
## XANPAGTX0501_000005-T1 17.0 22.0 27.0 19.0 56.0 16.0 17.0
## KS48XB3 KS9XB1 KS9XB2 KS9XB3
## XANPAGTX0501_000001-T1 464.0 376.0 297.0 323.5
## XANPAGTX0501_000002-T1 236.5 98.0 90.0 106.0
## XANPAGTX0501_000003-T1 209.0 313.5 216.5 268.5
## XANPAGTX0501_000004-T1 37.5 91.5 36.0 78.5
## XANPAGTX0501_000005-T1 6.0 24.0 21.0 21.0
# create new column, "max" for the max read count in each row
d$max<-apply(d,1,max)
min(d$max)
## [1] 0
d1<-d[which(d$max>=5),] #to remove lowly expressed genes, keep rows in which max read count across whole panel is atleast 5
# drop the max column, as its not needed anymore
raw_counts<-d1 %>% select(-max)
length(rownames(d1)) # total number of genes
## [1] 11105
length(rownames(raw_counts)) # number after removal of lowly expressed genes
## [1] 11105
dge <- DGEList(counts=raw_counts)
dge <- calcNormFactors(dge) # perform scale normalization, adjusting for differences
#group as replicates together
colnames(raw_counts)
## [1] "XBC2" "XBA1" "XSA2_2" "XSC1" "XSE2" "XBE1" "XTA2"
## [8] "XSC2" "XSA2" "XBA2" "XBC1" "XTA1" "XSA1" "XTC2"
## [15] "XTE2" "XBE2" "XMC2" "S_21XB1" "KS21XB1" "S_21XB3" "S_42XB1"
## [22] "S_42XB2" "S_42XB3" "KS48XB1" "KS48XB2" "KS48XB3" "KS9XB1" "KS9XB2"
## [29] "KS9XB3"
group=c(rep("1",17),rep("2",12)) # 17 samples for lichen and 12 for Xanthoria culture
design=model.matrix(~0+group)
colnames(design)=gsub("","",colnames(design))
head(design)
## group1 group2
## 1 1 0
## 2 1 0
## 3 1 0
## 4 1 0
## 5 1 0
## 6 1 0
v=voom(dge,design,plot=TRUE,normalize.method="none")
head(v)
## An object of class "EList"
## $targets
## group lib.size norm.factors
## XBC2 1 17504370 0.982611
## XBA1 1 16580337 1.072634
## XSA2_2 1 21037203 1.066389
## XSC1 1 13863356 1.002658
## XSE2 1 17230419 1.025860
## 24 more rows ...
##
## $E
## XBC2 XBA1 XSA2_2 XSC1 XSE2 XBE1
## XANPAGTX0501_000001-T1 3.949841 5.013341 4.819448 4.163897 4.285431 4.2142638
## XANPAGTX0501_000002-T1 3.473983 2.987517 3.759947 3.020576 3.319379 3.0916848
## XANPAGTX0501_000003-T1 3.455319 4.203627 3.654977 3.464183 4.065542 4.5634367
## XANPAGTX0501_000004-T1 2.853350 1.408030 2.512019 2.137533 1.250666 1.1711193
## XANPAGTX0501_000005-T1 1.137143 3.752729 3.396292 2.722495 1.159901 0.3993883
## XANPAGTX0501_000006-T1 3.553351 4.701815 4.534387 3.670320 3.388969 2.4764645
## XTA2 XSC2 XSA2 XBA2 XBC1 XTA1
## XANPAGTX0501_000001-T1 4.697926 4.292915 4.911517 4.723220 4.547046 4.767669
## XANPAGTX0501_000002-T1 3.788800 3.123545 3.655178 3.599775 2.551478 3.381120
## XANPAGTX0501_000003-T1 4.154783 3.896987 3.717913 3.183454 4.724350 4.594272
## XANPAGTX0501_000004-T1 2.237004 1.456414 2.362997 4.065836 1.662182 1.804195
## XANPAGTX0501_000005-T1 3.840968 2.570671 3.651165 3.667413 1.225118 4.506483
## XANPAGTX0501_000006-T1 4.154783 4.033428 4.487505 4.526786 3.041954 4.633706
## XSA1 XTC2 XTE2 XBE2 XMC2
## XANPAGTX0501_000001-T1 4.343970 4.458966 4.349140 3.63444726 4.6036306
## XANPAGTX0501_000002-T1 3.660943 3.587459 3.674020 2.90474967 2.9646127
## XANPAGTX0501_000003-T1 3.379259 4.466850 4.474055 3.63444726 4.6498169
## XANPAGTX0501_000004-T1 2.526965 1.688681 1.061274 1.83798066 0.9454191
## XANPAGTX0501_000005-T1 3.926182 2.883852 2.805435 0.02301255 1.5131036
## XANPAGTX0501_000006-T1 4.223676 3.783264 3.453591 3.16899185 3.2724905
## S_21XB1 KS21XB1 S_21XB3 S_42XB1 S_42XB2
## XANPAGTX0501_000001-T1 5.3698625 3.9723515 5.3144321 4.6923287 4.400417
## XANPAGTX0501_000002-T1 1.9837104 2.6599148 1.4443190 2.8576461 2.095689
## XANPAGTX0501_000003-T1 3.1655488 3.4874007 2.9844273 3.5624484 3.684210
## XANPAGTX0501_000004-T1 -0.5588168 3.4604965 1.2890408 1.9774859 2.633584
## XANPAGTX0501_000005-T1 0.4094743 -0.1415395 0.3214623 0.6503211 0.304276
## XANPAGTX0501_000006-T1 2.7055238 2.6179208 2.6813582 2.9188100 2.626204
## S_42XB3 KS48XB1 KS48XB2 KS48XB3 KS9XB1
## XANPAGTX0501_000001-T1 4.353708 4.5581293 4.641683 4.6067886 4.2674127
## XANPAGTX0501_000002-T1 2.073601 3.5195694 3.254421 3.6359970 2.3329584
## XANPAGTX0501_000003-T1 3.642113 3.3577632 3.531649 3.4580602 4.0055273
## XANPAGTX0501_000004-T1 2.195856 1.1878381 1.310377 0.9951813 2.2344686
## XANPAGTX0501_000005-T1 1.694107 -0.2271993 -0.083902 -1.5523065 0.3256164
## XANPAGTX0501_000006-T1 2.608638 2.9231634 2.746817 2.7302474 2.8141944
## KS9XB2 KS9XB3
## XANPAGTX0501_000001-T1 4.2245098 4.0729960
## XANPAGTX0501_000002-T1 2.5076099 2.4678556
## XANPAGTX0501_000003-T1 3.7693152 3.8046083
## XANPAGTX0501_000004-T1 1.1975885 2.0369267
## XANPAGTX0501_000005-T1 0.4340287 0.1594107
## XANPAGTX0501_000006-T1 3.1005211 3.1211633
##
## $weights
## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
## [1,] 4.570805 4.407244 5.170641 3.903719 4.522890 4.218450 4.772853 4.407200
## [2,] 2.639134 2.534159 3.019856 2.218091 2.608050 2.415787 2.766852 2.534132
## [3,] 3.716200 3.579559 4.210421 3.158393 3.675795 3.423309 3.882575 3.579524
## [4,] 1.300018 1.252259 1.481286 1.111546 1.285817 1.198589 1.359986 1.252247
## [5,] 1.756152 1.687120 2.015189 1.480036 1.735715 1.608629 1.842407 1.687102
## [6,] 3.397406 3.269922 3.856297 2.874701 3.359695 3.123404 3.552558 3.269889
## [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
## [1,] 3.984487 4.204313 3.911148 4.514136 3.722192 4.410126 4.001358 3.793217
## [2,] 2.268205 2.406889 2.222695 2.602376 2.104255 2.535971 2.278688 2.148339
## [3,] 3.226074 3.411221 3.164889 3.668415 3.001478 3.581922 3.240097 3.061923
## [4,] 1.133557 1.194570 1.113571 1.283223 1.062766 1.253078 1.138152 1.081391
## [5,] 1.512720 1.602744 1.483040 1.731985 1.407440 1.688312 1.519543 1.435412
## [6,] 2.938432 3.112056 2.880719 3.352809 2.729426 3.272126 2.951570 2.785368
## [,17] [,18] [,19] [,20] [,21] [,22] [,23]
## [1,] 4.032381 4.6453869 5.0706178 4.8407064 4.7521303 4.4319365 4.7410953
## [2,] 2.297977 1.7400493 1.9180691 1.8210324 1.7842532 1.6522669 1.7796774
## [3,] 3.265889 2.8705389 3.1563260 3.0003947 2.9419290 2.7251756 2.9346514
## [4,] 1.146598 1.1177753 1.2189049 1.1632269 1.1426243 1.0684088 1.1400565
## [5,] 1.532071 0.6361116 0.6765939 0.6544587 0.6461746 0.6162353 0.6451384
## [6,] 2.975740 1.9602083 2.1622770 2.0519603 2.0106587 1.8597449 2.0055200
## [,24] [,25] [,26] [,27] [,28] [,29]
## [1,] 5.0724342 4.9370964 5.0282623 5.1138836 4.4552933 5.061281
## [2,] 1.9188386 1.8616209 1.9001383 1.9364084 1.6617183 1.914115
## [3,] 3.1575617 3.0656324 3.1275260 3.1849705 2.7406688 3.149975
## [4,] 1.2193459 1.1864903 1.2086211 1.2294107 1.0735971 1.216638
## [5,] 0.6767716 0.6636186 0.6724436 0.6808214 0.6183553 0.675680
## [6,] 2.1631522 2.0980854 2.1418842 2.1831366 1.8704487 2.157779
##
## $design
## group1 group2
## 1 1 0
## 2 1 0
## 3 1 0
## 4 1 0
## 5 1 0
## 24 more rows ...
#MDS plot
cols<-c(rep("darkgreen",17),rep("tan",12)) # green for lichen and brown for xanthoria samples
plotMDS(v, labels = colnames(v),main="min5readcounts_in_any_sample",cex=0.75,col=cols)
#for calculation of DEGs
fit<-lmFit(v,design) # fits row-wise linear models (this will need the voom output file and the design matrix)
fit
## An object of class "MArrayLM"
## $coefficients
## group1 group2
## XANPAGTX0501_000001-T1 4.468067 4.5350839
## XANPAGTX0501_000002-T1 3.340491 2.5842564
## XANPAGTX0501_000003-T1 4.018468 3.5382874
## XANPAGTX0501_000004-T1 1.948324 1.6722398
## XANPAGTX0501_000005-T1 2.571747 0.1806385
## 11100 more rows ...
##
## $stdev.unscaled
## group1 group2
## XANPAGTX0501_000001-T1 0.1174059 0.1311368
## XANPAGTX0501_000002-T1 0.1550407 0.2137446
## XANPAGTX0501_000003-T1 0.1303573 0.1665387
## XANPAGTX0501_000004-T1 0.2200666 0.2674036
## XANPAGTX0501_000005-T1 0.1899151 0.3566337
## 11100 more rows ...
##
## $sigma
## [1] 0.8334902 0.7162065 0.7798425 0.9565603 1.3891010
## 11100 more elements ...
##
## $df.residual
## [1] 27 27 27 27 27
## 11100 more elements ...
##
## $cov.coefficients
## group1 group2
## group1 0.05882353 0.00000000
## group2 0.00000000 0.08333333
##
## $pivot
## [1] 1 2
##
## $rank
## [1] 2
##
## $Amean
## XANPAGTX0501_000001-T1 XANPAGTX0501_000002-T1 XANPAGTX0501_000003-T1
## 4.491424 3.013036 3.818495
## XANPAGTX0501_000004-T1 XANPAGTX0501_000005-T1
## 1.825576 1.568107
## 11100 more elements ...
##
## $method
## [1] "ls"
##
## $design
## group1 group2
## 1 1 0
## 2 1 0
## 3 1 0
## 4 1 0
## 5 1 0
## 24 more rows ...
#define comparisons as contrast matrices, which are basically AvsB for DEG calculation eg Lichen vs Xanthoria
contrast.matrix= makeContrasts(group1-group2,levels=design) # more comparisons can be provided here, based on the design
fit2= contrasts.fit(fit, contrast.matrix)
fit2= eBayes(fit2) # empirical Bayes statistics for differential expression
fit2
## An object of class "MArrayLM"
## $coefficients
## Contrasts
## group1 - group2
## XANPAGTX0501_000001-T1 -0.06701675
## XANPAGTX0501_000002-T1 0.75623463
## XANPAGTX0501_000003-T1 0.48018012
## XANPAGTX0501_000004-T1 0.27608455
## XANPAGTX0501_000005-T1 2.39110851
## 11100 more rows ...
##
## $stdev.unscaled
## Contrasts
## group1 - group2
## XANPAGTX0501_000001-T1 0.1760142
## XANPAGTX0501_000002-T1 0.2640537
## XANPAGTX0501_000003-T1 0.2114903
## XANPAGTX0501_000004-T1 0.3463149
## XANPAGTX0501_000005-T1 0.4040486
## 11100 more rows ...
##
## $sigma
## [1] 0.8334902 0.7162065 0.7798425 0.9565603 1.3891010
## 11100 more elements ...
##
## $df.residual
## [1] 27 27 27 27 27
## 11100 more elements ...
##
## $cov.coefficients
## Contrasts
## Contrasts group1 - group2
## group1 - group2 0.1421569
##
## $pivot
## [1] 1 2
##
## $rank
## [1] 2
##
## $Amean
## XANPAGTX0501_000001-T1 XANPAGTX0501_000002-T1 XANPAGTX0501_000003-T1
## 4.491424 3.013036 3.818495
## XANPAGTX0501_000004-T1 XANPAGTX0501_000005-T1
## 1.825576 1.568107
## 11100 more elements ...
##
## $method
## [1] "ls"
##
## $design
## group1 group2
## 1 1 0
## 2 1 0
## 3 1 0
## 4 1 0
## 5 1 0
## 24 more rows ...
##
## $contrasts
## Contrasts
## Levels group1 - group2
## group1 1
## group2 -1
##
## $df.prior
## [1] 2.871922
##
## $s2.prior
## [1] 0.7537697
##
## $var.prior
## [1] 8.68376
##
## $proportion
## [1] 0.01
##
## $s2.post
## [1] 0.7003844 0.5361043 0.6221539 0.8995059 1.8165558
## 11100 more elements ...
##
## $t
## Contrasts
## group1 - group2
## XANPAGTX0501_000001-T1 -0.4549539
## XANPAGTX0501_000002-T1 3.9114667
## XANPAGTX0501_000003-T1 2.8784901
## XANPAGTX0501_000004-T1 0.8405605
## XANPAGTX0501_000005-T1 4.3907758
## 11100 more rows ...
##
## $df.total
## [1] 29.87192 29.87192 29.87192 29.87192 29.87192
## 11100 more elements ...
##
## $p.value
## Contrasts
## group1 - group2
## XANPAGTX0501_000001-T1 0.6524317629
## XANPAGTX0501_000002-T1 0.0004894221
## XANPAGTX0501_000003-T1 0.0073148659
## XANPAGTX0501_000004-T1 0.4072722622
## XANPAGTX0501_000005-T1 0.0001301997
## 11100 more rows ...
##
## $lods
## Contrasts
## group1 - group2
## XANPAGTX0501_000001-T1 -7.3086114
## XANPAGTX0501_000002-T1 -0.6907942
## XANPAGTX0501_000003-T1 -3.4750901
## XANPAGTX0501_000004-T1 -6.3872391
## XANPAGTX0501_000005-T1 0.9125933
## 11100 more rows ...
##
## $F
## [1] 0.2069830 15.2995715 8.2857052 0.7065419 19.2789120
## 11100 more elements ...
##
## $F.p.value
## [1] 0.6524317629 0.0004894221 0.0073148659 0.4072722622 0.0001301997
## 11100 more elements ...
# see contrast matrix. in the example, coef=1 means first comparison (group1-group2 above)
complete_table=topTable(fit2, coef=1,number=nrow(v)) #make sure to change "coeff" is changed each time for each comparison
write.table(complete_table,"../analysis_and_temp_files/08_dge_culture_lichen/complete_lich_vs_xan.tsv", append="false", sep = "\t", quote=F)
plot(complete_table[,"logFC"],-log10(complete_table[,"adj.P.Val"]), main="Volcano_condition_Lich_vs_Xan")
abline(v=c(2,-2),lty=3,col="red",lwd=2)
abline(h=-log10(0.05),lty=3,col="red",lwd=2)
funannot<-read.delim2("../../02_long_read_assemblies/analysis_and_temp_files/06_annotate_lecanoro/Annotation_with_OG.txt",sep="\t")
complete_table2<-complete_table %>% rownames_to_column(var = "TranscriptID") %>%
left_join(funannot) %>% select(-c(PFAM,InterPro,EggNog,COG,GO.Terms,Secreted,Protease,CAZyme,CDS.transcript,Translation,gDNA,mRNA))
## Joining with `by = join_by(TranscriptID)`
upreg2=complete_table2[complete_table2[,"logFC"]>=2&complete_table2[,"adj.P.Val"]<=0.05,]
downreg2=complete_table2[complete_table2[,"logFC"]<=-2&complete_table2[,"adj.P.Val"]<=0.05,]
write.table(upreg2, "../analysis_and_temp_files/08_dge_culture_lichen/upreg_in_lichen_edgeR.txt", append="false", sep = "\t", quote=F, row.names = F)
write.table(downreg2, "../analysis_and_temp_files/08_dge_culture_lichen/upreg_in_culture_edgeR.txt", append="false", sep = "\t", quote=F, row.names = F)
###make table with GO annotations
go_df <-funannot %>% select(TranscriptID,GO.Terms_new) %>%
mutate(GO.Terms_new = strsplit(GO.Terms_new, ",")) %>%
unnest(GO.Terms_new) %>%
mutate(GO.Terms=sub(".*? ", "", GO.Terms_new),
short_term = substr(GO.Terms, 1,40))
go_data <- list(
term2protein = data.frame(
term = go_df$GO.Terms_new,
gene = go_df$TranscriptID
),
term2name = data.frame(
term = go_df$GO.Terms_new,
name = go_df$short_term
),
universe = unique(as.character(go_df$TranscriptID))
)
### select genes upregulated in lichens and order them by fold change
geneList1 = upreg2$logFC
names(geneList1) = as.character(upreg2$TranscriptID)
geneList1 = sort(geneList1, decreasing = TRUE)
geneList1 <- names(geneList1)
###enrichment analysis
enrich1<-clusterProfiler::enricher(geneList1,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=go_data$universe,
TERM2GENE=go_data$term2protein,
TERM2NAME=go_data$term2name)
enrichplot::dotplot(enrich1,showCategory=40,label_format=40)
enrich1_peirwise<-enrichplot::pairwise_termsim(enrich1)
enrichplot::emapplot(enrich1_peirwise)
### select genes upregulated in culture and order them by fold change
geneList2 = downreg2$logFC
names(geneList2) = as.character(downreg2$TranscriptID)
geneList2 = sort(geneList2, decreasing = TRUE)
geneList2 <- names(geneList2)
###enrichment analysis
enrich2<-clusterProfiler::enricher(geneList2,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=go_data$universe,
TERM2GENE=go_data$term2protein,
TERM2NAME=go_data$term2name)
enrichplot::dotplot(enrich2,showCategory=40,label_format=40)
enrich2_peirwise<-enrichplot::pairwise_termsim(enrich2)
enrichplot::emapplot(enrich2_peirwise)
###make table with IPS annotations
ips_df <-funannot %>% select(TranscriptID,InterPro_new) %>%
mutate(InterPro_new = strsplit(InterPro_new, ", I")) %>%
unnest(InterPro_new) %>% mutate(InterPro_new=str_replace(InterPro_new,"^PR","IPR")) %>%
mutate(short_term = substr(InterPro_new, 1,40))
ips_data <- list(
term2protein = data.frame(
term = ips_df$InterPro_new,
gene = ips_df$TranscriptID
),
term2name = data.frame(
term = ips_df$InterPro_new,
name = ips_df$short_term
),
universe = unique(as.character(ips_df$TranscriptID))
)
###enrichment analysis
enrich3<-clusterProfiler::enricher(geneList1,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=ips_data$universe,
TERM2GENE=ips_data$term2protein,
TERM2NAME=ips_data$term2name)
enrichplot::dotplot(enrich3,showCategory=40,label_format=40)
enrich4<-clusterProfiler::enricher(geneList2,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=ips_data$universe,
TERM2GENE=ips_data$term2protein,
TERM2NAME=ips_data$term2name)
enrichplot::dotplot(enrich4,showCategory=40,label_format=40)
(funannot %>% filter(grepl("036770",InterPro)) %>% nrow()) / (funannot %>% nrow()) have this annotation(upreg2 %>% filter(grepl("036770",InterPro)) %>% nrow()) / (upreg2 %>% nrow())(funannot %>% filter(grepl("036770",InterPro)) %>% nrow()) / (funannot %>% nrow())upreg2 %>% filter(TranscriptID %in% downreg2$TranscriptID)
## [1] TranscriptID logFC AveExpr t P.Value
## [6] adj.P.Val B GeneID Feature Contig
## [11] Start Stop Strand Name Product
## [16] Alias.Synonyms EC_number BUSCO Membrane antiSMASH
## [21] Notes ProtID CAZyme_new COG_new EggNog_new
## [26] GO.Terms_new InterPro_new PFAM_new Protease_new Secreted_new
## [31] KO
## <0 rows> (or 0-length row.names)
downreg2 %>% filter(TranscriptID %in% upreg2$TranscriptID)
## [1] TranscriptID logFC AveExpr t P.Value
## [6] adj.P.Val B GeneID Feature Contig
## [11] Start Stop Strand Name Product
## [16] Alias.Synonyms EC_number BUSCO Membrane antiSMASH
## [21] Notes ProtID CAZyme_new COG_new EggNog_new
## [26] GO.Terms_new InterPro_new PFAM_new Protease_new Secreted_new
## [31] KO
## <0 rows> (or 0-length row.names)
../10_lichen_effectorseff_list<-read.delim2("../../10_lichen_effectors/analysis_and_temp_files/02_characterize_predicted/annotation_predicted_effectors.txt")
eff_list$TranscriptID<-str_replace(eff_list$TranscriptID,"FUN","XANPAGTX0501")
eff_list %>% filter(TranscriptID %in% upreg2$TranscriptID) %>%
kable(format = "html", col.names = colnames(eff_list )) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | Product | EC_number | PFAM_new | InterPro_new | EggNog_new | COG_new | GO.Terms_new | Protease_new | CAZyme_new | antiSMASH | KO |
|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_000656-T1 | hypothetical protein | IPR000772 Ricin B, lectin domain, IPR035992 Ricin B-like lectins | |||||||||
| XANPAGTX0501_001015-T1 | hypothetical protein | PF00967, PF03330 | IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily | ENOG503P58T, ENOG503P74E, ENOG503P76M | S:(S) Function unknown | GO_process: GO:0042742 - defense response to bacterium [Evidence IEA], GO_process: GO:0050832 - defense response to fungus [Evidence IEA] | |||||
| XANPAGTX0501_001063-T1 | hypothetical protein | Cluster_1 | |||||||||
| XANPAGTX0501_001856-T1 | hypothetical protein | IPR037176 Osmotin/thaumatin-like superfamily | ENOG503P50I | ||||||||
| XANPAGTX0501_002409-T1 | hypothetical protein | IPR001338 Hydrophobin | GO_component: GO:0009277 - fungal-type cell wall [Evidence IEA], GO_function: GO:0005199 - structural constituent of cell wall [Evidence IEA] | ||||||||
| XANPAGTX0501_003287-T1 | hypothetical protein | Cluster_4 | |||||||||
| XANPAGTX0501_005364-T1 | hypothetical protein | ||||||||||
| XANPAGTX0501_005573-T1 | hypothetical protein | ||||||||||
| XANPAGTX0501_005675-T1 | hypothetical protein | PF05572, PF13688 | IPR008754 Peptidase M43, pregnancy-associated plasma-A, IPR024079 Metallopeptidase, catalytic domain superfamily | ENOG503NZAM | O:(O) Posttranslational modification, protein turnover, chaperones | GO_function: GO:0008237 - metallopeptidase activity [Evidence IEA] | M43B | ||||
| XANPAGTX0501_006142-T1 | hypothetical protein | ||||||||||
| XANPAGTX0501_006194-T1 | hypothetical protein | 3.2.1.78 | IPR036908 RlpA-like domain superfamily | ENOG503P7ES | O:(O) Posttranslational modification, protein turnover, chaperones | ||||||
| XANPAGTX0501_006245-T1 | hypothetical protein | ||||||||||
| XANPAGTX0501_006291-T1 | hypothetical protein | Cluster_1 | |||||||||
| XANPAGTX0501_006967-T1 | hypothetical protein | ||||||||||
| XANPAGTX0501_008875-T1 | hypothetical protein | ||||||||||
| XANPAGTX0501_009026-T1 | hypothetical protein | ||||||||||
| XANPAGTX0501_009189-T1 | hypothetical protein | ||||||||||
| XANPAGTX0501_009606-T1 | hypothetical protein | IPR011024 Gamma-crystallin-like | ENOG503PMNB | ||||||||
| XANPAGTX0501_009688-T1 | hypothetical protein | PF00734 | IPR000254 Cellulose-binding domain, fungal, IPR035971 Cellulose-binding domain superfamily, IPR036908 RlpA-like domain superfamily | GO_component: GO:0005576 - extracellular region [Evidence IEA], GO_function: GO:0030248 - cellulose binding [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | |||||||
| XANPAGTX0501_009886-T1 | hypothetical protein | ||||||||||
| XANPAGTX0501_010250-T1 | hypothetical protein | ENOG503P3M4 | |||||||||
| XANPAGTX0501_010470-T1 | hypothetical protein | 3.2.1.17 | PF00959 | IPR002196 Glycoside hydrolase, family 24, IPR009045 Hedgehog signalling/DD-peptidase zinc-binding domain superfamily, IPR023346 Lysozyme-like domain superfamily, IPR033907 Endolysin/autolysin, IPR034690 Endolysin T4 type | ENOG503P2E0, ENOG503P2RE | O:(O) Posttranslational modification, protein turnover, chaperones | GO_function: GO:0003796 - lysozyme activity [Evidence IEA], GO_process: GO:0009253 - peptidoglycan catabolic process [Evidence IEA], GO_process: GO:0016998 - cell wall macromolecule catabolic process [Evidence IEA], GO_process: GO:0019076 - viral release from host cell [Evidence IEA], GO_process: GO:0019835 - cytolysis [Evidence IEA] | GH24 | Cluster_1 | K01185 |
eff_list %>% filter(TranscriptID %in% downreg2$TranscriptID) %>%
kable(format = "html", col.names = colnames(eff_list)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | Product | EC_number | PFAM_new | InterPro_new | EggNog_new | COG_new | GO.Terms_new | Protease_new | CAZyme_new | antiSMASH | KO |
|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_000850-T1 | hypothetical protein | ENOG503P7C3 | |||||||||
| XANPAGTX0501_005118-T1 | hypothetical protein | ENOG503PWV2, ENOG503PYSR | Cluster_1 | ||||||||
| XANPAGTX0501_006848-T1 | hypothetical protein | Cluster_1 | |||||||||
| XANPAGTX0501_009170-T1 | hypothetical protein | PF02015 | IPR000334 Glycoside hydrolase, family 45, IPR036908 RlpA-like domain superfamily | ENOG503P08U, ENOG503Q3X3 | G:(G) Carbohydrate transport and metabolism | GO_function: GO:0008810 - cellulase activity [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | GH45 | ||||
| XANPAGTX0501_010442-T1 | hypothetical protein | ||||||||||
| XANPAGTX0501_010474-T1 | hypothetical protein | IPR008979 Galactose-binding-like domain superfamily | Cluster_1 |
library(sleuth)
kal_dirs <- data.frame("sample"=metadata$run_id, "condition"=metadata$sample_type,
"path"=paste0("../analysis_and_temp_files/06_meta_mapping/kallisto_meta_mapping/",metadata$run_id,"_kallisto")) %>% filter(sample!="MP_II" & sample!="MP_I")
#define list of genes to be included: only mycobiont and only those that have read count across whole panel of >=5
target_id<-rownames(d1)
so <- sleuth_prep(kal_dirs, extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## .............................
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11105 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## .............................
so <- sleuth_fit(so, ~condition, 'full')
## fitting measurement error models
## shrinkage estimation
## 16 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000408-T1, XANPAGTX0501_000967-T1, XANPAGTX0501_000968-T1, XANPAGTX0501_000969-T1, XANPAGTX0501_000980-T1, XANPAGTX0501_000995-T1, XANPAGTX0501_002621-T1, XANPAGTX0501_002938-T1, XANPAGTX0501_004237-T1, XANPAGTX0501_005100-T1, XANPAGTX0501_008798-T1, XANPAGTX0501_009179-T1, XANPAGTX0501_010285-T1, XANPAGTX0501_010514-T1, XANPAGTX0501_010642-T1, XANPAGTX0501_010694-T1
## computing variance of betas
so <- sleuth_fit(so, ~1, 'reduced')
## fitting measurement error models
## shrinkage estimation
## 16 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000408-T1, XANPAGTX0501_000967-T1, XANPAGTX0501_000968-T1, XANPAGTX0501_000969-T1, XANPAGTX0501_000980-T1, XANPAGTX0501_000995-T1, XANPAGTX0501_002621-T1, XANPAGTX0501_002938-T1, XANPAGTX0501_004237-T1, XANPAGTX0501_005100-T1, XANPAGTX0501_008798-T1, XANPAGTX0501_009179-T1, XANPAGTX0501_010285-T1, XANPAGTX0501_010514-T1, XANPAGTX0501_010642-T1, XANPAGTX0501_010694-T1
## computing variance of betas
so <- sleuth_lrt(so, 'reduced', 'full')
so <- sleuth_wt(so, 'conditionxanthoria_culture')
plot_pca(so, color_by = 'condition', text_labels = TRUE,use_filtered=T)
sleuth_table <- sleuth_results(so, 'conditionxanthoria_culture')
sig <- sleuth_table %>% tibble::as_tibble() %>%
filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>%
arrange(desc(b)) %>% mutate(change = if_else(b > 1, "culture", ifelse(b< -1, "lichen", "low_logFC")))
table(sig$change)
##
## culture lichen low_logFC
## 564 1185 4124
pca<-plot_pca(so, color_by = 'condition', text_labels = F,use_filtered=T)
pca+theme_bw()+theme(text=element_text(size=7))
ggsave('../results/lichen_culture_pca.pdf',width = 4.5, height = 3)
plot_pc_variance(so)
sig2<-sig %>% left_join(funannot, by=c("target_id"="TranscriptID"))
upreg_sl=sig2 %>% filter(change=="lichen") %>% select(-c(CDS.transcript,Translation,gDNA,mRNA))
downreg_sl=sig2 %>% filter(change=="culture")%>% select(-c(CDS.transcript,Translation,gDNA,mRNA))
write.table(upreg_sl, "../analysis_and_temp_files/08_dge_culture_lichen/upreg_in_lichen_sleuth.txt", append="false", sep = "\t", quote=F, row.names = F)
write.table(downreg_sl, "../analysis_and_temp_files/08_dge_culture_lichen/upreg_in_culture_sleuth.txt", append="false", sep = "\t", quote=F, row.names = F)
tabd_df <- so$obs_norm[so$obs_norm$target_id %in% target_id,]
tabd_df <- dplyr::select(tabd_df, target_id, sample,
tpm)
tabd_df <- reshape2::dcast(tabd_df, target_id ~ sample,
value.var = "tpm")
write.table(tabd_df, "../analysis_and_temp_files/08_dge_culture_lichen/norm_counts_sleuth.txt", append="false", sep = "\t", quote=F, row.names = F)
library(ggVennDiagram)
##
## Attaching package: 'ggVennDiagram'
## The following object is masked from 'package:tidyr':
##
## unite
venn_lichen<-list(egdeR = upreg2$TranscriptID,
sleuth = sig$target_id[sig$change=="lichen"])
l<-ggVennDiagram(venn_lichen,label_size = 5,set_size=5)+labs(title = "Upregulated in lichen")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
l
upreg_viz<-sig %>% filter(b<0) %>%
mutate(edgeR = ifelse(target_id %in% upreg2$TranscriptID,"upregulated_in_edgeR","not_upregulated_in_edgeR"))
ggplot(upreg_viz)+geom_density(aes(x=b,fill=edgeR))+facet_wrap(.~edgeR,nrow = 2)
venn_cult<-list(egdeR = downreg2$TranscriptID,
sleuth = sig$target_id[sig$change=="culture"])
c<-ggVennDiagram(venn_cult,label_size = 5,set_size=5)+labs(title = "Upregulated in culture")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
c
down_viz<-sig %>% filter(b>0) %>%
mutate(edgeR = ifelse(target_id %in% downreg2$TranscriptID,"upregulated_in_edgeR","not_upregulated_in_edgeR"))
ggplot(down_viz)+geom_density(aes(x=b,fill=edgeR))+facet_wrap(.~edgeR,nrow = 2)
plot_bootstrap(so,
target_id = sig$target_id[which.max(sig$b)],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = sig$target_id[which.min(sig$b)],
units = "est_counts",
color_by = "condition")
sig$b[which.min(abs(sig$b))] and the q-value (p-value adjusted for multiple test correction) is sig$qval[which.min(abs(sig$b))], but you can see the difference between sample types somewhatplot_bootstrap(so,
target_id = sig$target_id[which.min(abs(sig$b))],
units = "est_counts",
color_by = "condition")
### select genes upregulated in lichens and order them by fold change
geneList5 = sig$b[sig$change=="lichen"]
names(geneList5) = sig$target_id[sig$change=="lichen"]
geneList5 = sort(geneList5, decreasing = F)
geneList5 <- names(geneList5)
###enrichment analysis
enrich5<-clusterProfiler::enricher(geneList5,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=go_data$universe,
TERM2GENE=go_data$term2protein,
TERM2NAME=go_data$term2name)
enrichplot::dotplot(enrich5,showCategory=40,label_format=40)
enrich5_pairwise<-enrichplot::pairwise_termsim(enrich5)
enrichplot::emapplot(enrich5_pairwise)
### select genes upregulated in lichens and order them by fold change
geneList6 = sig$b[sig$change=="culture"]
names(geneList6) = sig$target_id[sig$change=="culture"]
geneList6 = sort(geneList6, decreasing = T)
geneList6 <- names(geneList6)
###enrichment analysis
enrich6<-clusterProfiler::enricher(geneList6,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=go_data$universe,
TERM2GENE=go_data$term2protein,
TERM2NAME=go_data$term2name)
enrichplot::dotplot(enrich6,showCategory=40,label_format=40)
enrich6_pairwise<-enrichplot::pairwise_termsim(enrich6)
enrichplot::emapplot(enrich6_pairwise)
enrich7<-clusterProfiler::enricher(geneList5,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=ips_data$universe,
TERM2GENE=ips_data$term2protein,
TERM2NAME=ips_data$term2name)
enrichplot::dotplot(enrich7,showCategory=40,label_format=40)
* Upregulated in lichen as a graph
enrich7_pairwise<-enrichplot::pairwise_termsim(enrich7)
enrichplot::emapplot(enrich7_pairwise)
pdf(file="../results/lichen_upr.pdf",width=5,height=4)
enrichplot::emapplot(enrich7_pairwise,cex_label_category=0.4,cex_line=0.25,
shadowtext=F,cex_pie2axis=0.1,repel=T)
dev.off()
## quartz_off_screen
## 2
enrich8<-clusterProfiler::enricher(geneList6,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=ips_data$universe,
TERM2GENE=ips_data$term2protein,
TERM2NAME=ips_data$term2name)
enrichplot::dotplot(enrich8,showCategory=40,label_format=40)
* Upregulated in culture as a graph
enrich8_pairwise<-enrichplot::pairwise_termsim(enrich8)
enrichplot::emapplot(enrich8_pairwise)
pdf(file="../results/culture_upr.pdf",width=5,height=4)
enrichplot::emapplot(enrich8_pairwise,cex_label_category=0.4,cex_line=0.25,
shadowtext=F,cex_pie2axis=0.1,repel=T)
dev.off()
## quartz_off_screen
## 2
perc<-funannot %>% mutate(go_annotated=ifelse(!(is.na(GO.Terms_new)),"Annotated","Non-annotated"),
ipr_annotated=ifelse(!(is.na(InterPro_new)),"Annotated","Non-annotated"),
gene_set=case_when(
TranscriptID %in% sig$target_id[sig$change=="culture"] ~ "Upregulated in culture",
TranscriptID %in% sig$target_id[sig$change=="lichen"] ~ "Upregulated in lichen",
T ~ "non-DGE"))
ipr_perc_dge<- perc %>% group_by(gene_set,ipr_annotated) %>% summarize(n=n()) %>% mutate(database="InterPro",annotated=ipr_annotated) %>% select(-ipr_annotated)
## `summarise()` has grouped output by 'gene_set'. You can override using the
## `.groups` argument.
go_perc_dge <- perc %>% group_by(gene_set,go_annotated) %>% summarize(n=n()) %>% mutate(database="GO",annotated=go_annotated) %>% select(-go_annotated)
## `summarise()` has grouped output by 'gene_set'. You can override using the
## `.groups` argument.
ipr_perc_all<- perc %>% group_by(ipr_annotated) %>% summarize(n=n()) %>% mutate(database="InterPro",gene_set="Whole transcriptome",annotated=ipr_annotated) %>% select(-ipr_annotated)
go_perc_all <- perc %>% group_by(go_annotated) %>% summarize(n=n()) %>% mutate(database="GO",gene_set="Whole transcriptome",annotated=go_annotated) %>% select(-go_annotated)
perc2<-rbind(ipr_perc_dge,go_perc_dge,ipr_perc_all,go_perc_all)
perc2$annotated<-factor(perc2$annotated,levels=c("Non-annotated","Annotated"))
ggplot(perc2 %>% filter(gene_set %in% c("Upregulated in culture","Upregulated in lichen")),
aes(x=database,y=n,fill=annotated))+geom_bar(position="stack",stat="identity")+
facet_wrap(~gene_set)
* Instead of two datatbases, visualize the number of proteins with any kind of functional annotation * NB: counted tRNA as being annotated
#make bar graph for DGE
perc<-funannot %>% mutate(annotated=ifelse(!(is.na(GO.Terms_new))| !(is.na(CAZyme_new))| !(is.na(PFAM_new))|
!(is.na(Protease_new))|!(is.na(InterPro_new))| KO!=""|Feature=="tRNA",
"Annotated","Non-annotated"),
gene_set=case_when(
TranscriptID %in% sig$target_id[sig$change=="culture"] ~ "Upregulated in culture",
TranscriptID %in% sig$target_id[sig$change=="lichen"] ~ "Upregulated in lichen",
T ~ "non-DGE"))
perc_dge<- perc %>% group_by(gene_set,annotated) %>% summarize(n=n()) %>%
group_by(gene_set) %>% mutate(perc=(100*n)/sum(n))
## `summarise()` has grouped output by 'gene_set'. You can override using the
## `.groups` argument.
dge_plot<-ggplot(perc_dge %>% filter(gene_set %in% c("Upregulated in culture","Upregulated in lichen")),
aes(x=gene_set,y=n,fill=annotated))+geom_bar(position="stack",stat="identity")+
geom_text(aes(label = paste0(round(perc,0),"%"),color=annotated), position=position_stack(vjust = 0.5),size=7)+
xlab("")+ylab("# of transcripts")+ggtitle("Differentially expressed")+
scale_fill_manual(values = c("Non-annotated"="#ffda73","Annotated"="#156902"))+
scale_color_manual(values = c("Non-annotated"="#156902","Annotated"="#ffda73"))+ theme_minimal()+
theme(legend.title=element_blank(),legend.position = c(0.2, 0.8),
legend.background = element_rect(fill="white",
linewidth=0.5, linetype="solid",
colour ="grey"),
panel.grid.major.x = element_blank(),
text = element_text(size=12),
axis.text=element_text(size=8))
#donut plot for the whole genome
perc_all <- perc %>% group_by(annotated) %>% summarize(n=n()) %>% mutate(perc=(100*n)/sum(n))
perc_all$ymax <- cumsum(perc_all$perc)
# Compute the bottom of each rectangle
perc_all$ymin <- c(0, head(perc_all$ymax, n=-1))
# Compute label position
perc_all$labelPosition <- (perc_all$ymax + perc_all$ymin) / 2
# Compute a good label
perc_all$label <- paste0(round(perc_all$perc,0), "%")
# Make the plot
all_plot<-ggplot(perc_all, aes(ymax=ymax, ymin=ymin, xmax=4, xmin=3, fill=annotated)) +
geom_rect() +
geom_text( x=3.5, aes(y=labelPosition, label=label,color=annotated), size=8) +
scale_fill_manual(values = c("Non-annotated"="#ffda73","Annotated"="#156902"))+
scale_color_manual(values = c("Non-annotated"="#156902","Annotated"="#ffda73"))+
coord_polar(theta="y") + ggtitle("Whole transcriptome (n = 11,185)")+
xlim(c(2, 4)) +
theme_void() +
theme(legend.position = "none",text = element_text(size=12))
library(patchwork)
dge_plot+all_plot
all_plot<-ggplot(perc_all, aes(ymax=ymax, ymin=ymin, xmax=4, xmin=3, fill=annotated)) +
geom_rect() +
geom_text( x=3.5, aes(y=labelPosition, label=label,color=annotated), size=2.75) +
scale_fill_manual(values = c("Non-annotated"="#ffda73","Annotated"="#156902"))+
scale_color_manual(values = c("Non-annotated"="#156902","Annotated"="#ffda73"))+
coord_polar(theta="y") + ggtitle("Whole transcriptome (n = 11,185)")+
xlim(c(2, 4)) +
theme_void() +
theme(legend.position = "none",text = element_text(size=8),plot.title = element_text(size=8))
dge_plot<-ggplot(perc_dge %>% filter(gene_set %in% c("Upregulated in culture","Upregulated in lichen")),
aes(x=gene_set,y=n,fill=annotated))+geom_bar(position="stack",stat="identity")+
geom_text(aes(label = paste0(round(perc,0),"%"),color=annotated), position=position_stack(vjust = 0.5),size=2.75)+
xlab("")+ylab("# of transcripts")+ggtitle("Differentially expressed")+
scale_fill_manual(values = c("Non-annotated"="#ffda73","Annotated"="#156902"))+
scale_color_manual(values = c("Non-annotated"="#156902","Annotated"="#ffda73"))+ theme_minimal()+
theme(legend.title=element_blank(),legend.position = c(0.2, 0.8),
legend.background = element_rect(fill="white",
linewidth=0.5, linetype="solid",
colour ="grey"),
panel.grid.major.x = element_blank(),
text = element_text(size=8),
axis.text=element_text(size=6),plot.title = element_text(size=8))
pdf(file="../results/annotated_percent.pdf",width=4.5,height=3.5)
dge_plot+all_plot
dev.off()
## quartz_off_screen
## 2
10_lichen effectors. Those are proteins identified as secreted by 3 tools and identified as effectors by 2 toolseff_list<- eff_list %>%
left_join(sig, by = c("TranscriptID"="target_id"))
eff_list %>% filter(change=="lichen") %>%
kable(format = "html", col.names = colnames(eff_list)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | Product | EC_number | PFAM_new | InterPro_new | EggNog_new | COG_new | GO.Terms_new | Protease_new | CAZyme_new | antiSMASH | KO | pval | qval | b | se_b | mean_obs | var_obs | tech_var | sigma_sq | smooth_sigma_sq | final_sigma_sq | change |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_000656-T1 | hypothetical protein | IPR000772 Ricin B, lectin domain, IPR035992 Ricin B-like lectins | 0.0000000 | 0.0000000 | -4.357565 | 0.4814432 | 5.9017838 | 6.3427509 | 0.0164185 | 1.6140872 | 0.0998084 | 1.6140872 | lichen | |||||||||
| XANPAGTX0501_001015-T1 | hypothetical protein | PF00967, PF03330 | IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily | ENOG503P58T, ENOG503P74E, ENOG503P76M | S:(S) Function unknown | GO_process: GO:0042742 - defense response to bacterium [Evidence IEA], GO_process: GO:0050832 - defense response to fungus [Evidence IEA] | 0.0000000 | 0.0000000 | -3.506517 | 0.4643931 | 5.2846088 | 4.5519407 | 0.0122602 | 1.5048031 | 0.1598182 | 1.5048031 | lichen | |||||
| XANPAGTX0501_001063-T1 | hypothetical protein | Cluster_1 | 0.0000000 | 0.0000000 | -4.589396 | 0.3736799 | 7.2076979 | 6.2387691 | 0.0049656 | 0.9773059 | 0.0431282 | 0.9773059 | lichen | |||||||||
| XANPAGTX0501_001856-T1 | hypothetical protein | IPR037176 Osmotin/thaumatin-like superfamily | ENOG503P50I | 0.0000000 | 0.0000000 | -3.823871 | 0.4267541 | 5.3759413 | 4.9088637 | 0.0242365 | 1.2568772 | 0.1485279 | 1.2568772 | lichen | ||||||||
| XANPAGTX0501_002041-T1 | hypothetical protein | 0.0000024 | 0.0000117 | -1.127546 | 0.2389993 | 4.1982488 | 0.4966441 | 0.0198173 | 0.1639853 | 0.3819970 | 0.3819970 | lichen | ||||||||||
| XANPAGTX0501_002409-T1 | hypothetical protein | IPR001338 Hydrophobin | GO_component: GO:0009277 - fungal-type cell wall [Evidence IEA], GO_function: GO:0005199 - structural constituent of cell wall [Evidence IEA] | 0.0000000 | 0.0000000 | -4.088717 | 0.2304978 | 9.5981869 | 4.5603784 | 0.0003597 | 0.3733771 | 0.0994788 | 0.3733771 | lichen | ||||||||
| XANPAGTX0501_003186-T1 | hypothetical protein | Cluster_1 | 0.0002443 | 0.0007831 | -1.045733 | 0.2850859 | 7.2273522 | 0.8260378 | 0.0009527 | 0.5707678 | 0.0428782 | 0.5707678 | lichen | |||||||||
| XANPAGTX0501_003287-T1 | hypothetical protein | Cluster_4 | 0.0000000 | 0.0000000 | -1.493602 | 0.1967691 | 4.7017340 | 0.7206409 | 0.0136889 | 0.1524257 | 0.2586729 | 0.2586729 | lichen | |||||||||
| XANPAGTX0501_005364-T1 | hypothetical protein | 0.0000000 | 0.0000000 | -4.400832 | 0.3864616 | 6.9122523 | 5.8787781 | 0.0054429 | 1.0451753 | 0.0488290 | 1.0451753 | lichen | ||||||||||
| XANPAGTX0501_005573-T1 | hypothetical protein | 0.0000000 | 0.0000000 | -2.506069 | 0.2266291 | 5.6609996 | 1.9262226 | 0.0095206 | 0.3517756 | 0.1192397 | 0.3517756 | lichen | ||||||||||
| XANPAGTX0501_005675-T1 | hypothetical protein | PF05572, PF13688 | IPR008754 Peptidase M43, pregnancy-associated plasma-A, IPR024079 Metallopeptidase, catalytic domain superfamily | ENOG503NZAM | O:(O) Posttranslational modification, protein turnover, chaperones | GO_function: GO:0008237 - metallopeptidase activity [Evidence IEA] | M43B | 0.0000000 | 0.0000000 | -2.825087 | 0.1615625 | 8.3760453 | 2.1821673 | 0.0005138 | 0.1831034 | 0.0515336 | 0.1831034 | lichen | ||||
| XANPAGTX0501_006142-T1 | hypothetical protein | 0.0000000 | 0.0000000 | -2.552912 | 0.1836978 | 6.0165771 | 1.8662663 | 0.0052380 | 0.2321399 | 0.0918787 | 0.2321399 | lichen | ||||||||||
| XANPAGTX0501_006194-T1 | hypothetical protein | 3.2.1.78 | IPR036908 RlpA-like domain superfamily | ENOG503P7ES | O:(O) Posttranslational modification, protein turnover, chaperones | 0.0000000 | 0.0000000 | -1.466337 | 0.1233940 | 5.8505478 | 0.6054853 | 0.0035018 | 0.0642183 | 0.1036059 | 0.1036059 | lichen | ||||||
| XANPAGTX0501_006245-T1 | hypothetical protein | 0.0000000 | 0.0000000 | -3.929116 | 0.4012715 | 4.2238012 | 4.9707307 | 0.0580619 | 1.0746222 | 0.3750018 | 1.0746222 | lichen | ||||||||||
| XANPAGTX0501_006291-T1 | hypothetical protein | Cluster_1 | 0.0000000 | 0.0000000 | -2.524612 | 0.4345364 | 1.9200532 | 2.4738155 | 0.1747462 | 0.7301201 | 1.1535179 | 1.1535179 | lichen | |||||||||
| XANPAGTX0501_006751-T1 | hypothetical protein | Cluster_4 | 0.0000000 | 0.0000000 | -1.137824 | 0.1152815 | 6.0347959 | 0.4150017 | 0.0027983 | 0.0902720 | 0.0906888 | 0.0906888 | lichen | |||||||||
| XANPAGTX0501_006967-T1 | hypothetical protein | 0.0000000 | 0.0000000 | -1.686952 | 0.1629173 | 6.9741854 | 0.8949974 | 0.0013260 | 0.1853835 | 0.0471902 | 0.1853835 | lichen | ||||||||||
| XANPAGTX0501_007280-T1 | hypothetical protein | 0.0000002 | 0.0000012 | -1.317948 | 0.2534485 | 5.7082083 | 0.8721158 | 0.0044510 | 0.4474169 | 0.1150951 | 0.4474169 | lichen | ||||||||||
| XANPAGTX0501_008875-T1 | hypothetical protein | 0.0050513 | 0.0117058 | -1.934027 | 0.6898007 | 0.8582434 | 4.1673621 | 0.0976534 | 3.2495299 | 1.4505443 | 3.2495299 | lichen | ||||||||||
| XANPAGTX0501_009026-T1 | hypothetical protein | 0.0000000 | 0.0000000 | -1.512207 | 0.2285639 | 5.9477612 | 0.9288757 | 0.0034740 | 0.3640176 | 0.0965398 | 0.3640176 | lichen | ||||||||||
| XANPAGTX0501_009189-T1 | hypothetical protein | 0.0000000 | 0.0000000 | -4.014594 | 0.3923972 | 2.3682678 | 4.8172641 | 0.0859581 | 0.7106675 | 0.9971806 | 0.9971806 | lichen | ||||||||||
| XANPAGTX0501_009311-T1 | hypothetical protein | PF05730 | IPR008427 Extracellular membrane protein, CFEM domain | 0.0000000 | 0.0000000 | -1.019264 | 0.1582712 | 7.0425826 | 0.4309233 | 0.0010038 | 0.1752083 | 0.0457542 | 0.1752083 | lichen | ||||||||
| XANPAGTX0501_009606-T1 | hypothetical protein | IPR011024 Gamma-crystallin-like | ENOG503PMNB | 0.0009831 | 0.0027450 | -2.529422 | 0.7675780 | 4.3477047 | 5.6039016 | 0.0639172 | 4.0806311 | 0.3420776 | 4.0806311 | lichen | ||||||||
| XANPAGTX0501_009688-T1 | hypothetical protein | PF00734 | IPR000254 Cellulose-binding domain, fungal, IPR035971 Cellulose-binding domain superfamily, IPR036908 RlpA-like domain superfamily | GO_component: GO:0005576 - extracellular region [Evidence IEA], GO_function: GO:0030248 - cellulose binding [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | 0.0000000 | 0.0000000 | -2.868656 | 0.1587323 | 5.5946483 | 2.2383423 | 0.0098738 | 0.1673667 | 0.1253745 | 0.1673667 | lichen | |||||||
| XANPAGTX0501_009886-T1 | hypothetical protein | 0.0000000 | 0.0000000 | -2.690801 | 0.4211666 | 2.0891440 | 2.6668573 | 0.1520313 | 0.7272087 | 1.0957544 | 1.0957544 | lichen | ||||||||||
| XANPAGTX0501_010250-T1 | hypothetical protein | ENOG503P3M4 | 0.0000000 | 0.0000000 | -1.956382 | 0.1621732 | 5.2525682 | 1.1399713 | 0.0084374 | 0.1765706 | 0.1640329 | 0.1765706 | lichen | |||||||||
| XANPAGTX0501_010470-T1 | hypothetical protein | 3.2.1.17 | PF00959 | IPR002196 Glycoside hydrolase, family 24, IPR009045 Hedgehog signalling/DD-peptidase zinc-binding domain superfamily, IPR023346 Lysozyme-like domain superfamily, IPR033907 Endolysin/autolysin, IPR034690 Endolysin T4 type | ENOG503P2E0, ENOG503P2RE | O:(O) Posttranslational modification, protein turnover, chaperones | GO_function: GO:0003796 - lysozyme activity [Evidence IEA], GO_process: GO:0009253 - peptidoglycan catabolic process [Evidence IEA], GO_process: GO:0016998 - cell wall macromolecule catabolic process [Evidence IEA], GO_process: GO:0019076 - viral release from host cell [Evidence IEA], GO_process: GO:0019835 - cytolysis [Evidence IEA] | GH24 | Cluster_1 | K01185 | 0.0000000 | 0.0000000 | -1.921148 | 0.2543482 | 5.5919285 | 1.3660764 | 0.0067217 | 0.4483603 | 0.1256340 | 0.4483603 | lichen |
lichen_eff<-eff_list$TranscriptID[eff_list$TranscriptID %in% sig$target_id[sig$change=="lichen"]]
plot_bootstrap(so,
target_id = lichen_eff[11],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = lichen_eff[7],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = lichen_eff[18],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = lichen_eff[20],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = lichen_eff[23],
units = "est_counts",
color_by = "condition")
* two odd ones: XANPAGTX0501_008875-T1, XANPAGTX0501_006291-T1
plot_bootstrap(so,
target_id = lichen_eff[15],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = lichen_eff[19],
units = "est_counts",
color_by = "condition")
eff_list %>% filter(change=="culture") %>%
kable(format = "html", col.names = colnames(eff_list)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | Product | EC_number | PFAM_new | InterPro_new | EggNog_new | COG_new | GO.Terms_new | Protease_new | CAZyme_new | antiSMASH | KO | pval | qval | b | se_b | mean_obs | var_obs | tech_var | sigma_sq | smooth_sigma_sq | final_sigma_sq | change |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_000850-T1 | hypothetical protein | ENOG503P7C3 | 0.0000000 | 0.0000000 | 2.534878 | 0.2622001 | 7.460813 | 2.0806559 | 0.0012183 | 0.4823944 | 0.0412653 | 0.4823944 | culture | |||||||||
| XANPAGTX0501_005118-T1 | hypothetical protein | ENOG503PWV2, ENOG503PYSR | Cluster_1 | 0.0000000 | 0.0000000 | 5.651733 | 0.6707321 | 2.530043 | 11.0765183 | 0.0109173 | 3.1537666 | 0.9389202 | 3.1537666 | culture | ||||||||
| XANPAGTX0501_006848-T1 | hypothetical protein | Cluster_1 | 0.0000000 | 0.0000000 | 3.980717 | 0.5309641 | 2.073824 | 5.8933957 | 0.0141339 | 1.9690481 | 1.1010599 | 1.9690481 | culture | |||||||||
| XANPAGTX0501_009170-T1 | hypothetical protein | PF02015 | IPR000334 Glycoside hydrolase, family 45, IPR036908 RlpA-like domain superfamily | ENOG503P08U, ENOG503Q3X3 | G:(G) Carbohydrate transport and metabolism | GO_function: GO:0008810 - cellulase activity [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | GH45 | 0.0039702 | 0.0094673 | 2.253664 | 0.7823812 | 5.814142 | 5.4281710 | 0.0376799 | 4.2682699 | 0.1064086 | 4.2682699 | culture | ||||
| XANPAGTX0501_010191-T1 | hypothetical protein | 3.1.1.74 | PF01083 | IPR000675 Cutinase/acetylxylan esterase, IPR011150 Cutinase, monofunctional, IPR029058 Alpha/Beta hydrolase fold | ENOG503P4Q7 | G:(G) Carbohydrate transport and metabolism | GO_component: GO:0005576 - extracellular region [Evidence IEA], GO_function: GO:0016787 - hydrolase activity [Evidence IEA], GO_function: GO:0050525 - cutinase activity [Evidence IEA] | CE5 | 0.0000009 | 0.0000045 | 1.151281 | 0.2338590 | 4.966704 | 0.7039702 | 0.0094855 | 0.3752306 | 0.2077829 | 0.3752306 | culture | |||
| XANPAGTX0501_010442-T1 | hypothetical protein | 0.0005211 | 0.0015524 | 1.618450 | 0.4664592 | 1.417648 | 1.6050501 | 0.2194048 | 0.7626476 | 1.3111874 | 1.3111874 | culture | ||||||||||
| XANPAGTX0501_010474-T1 | hypothetical protein | IPR008979 Galactose-binding-like domain superfamily | Cluster_1 | 0.0000000 | 0.0000000 | 3.724444 | 0.2985908 | 7.461490 | 4.0897241 | 0.0023959 | 0.6247736 | 0.0412642 | 0.6247736 | culture |
culture_eff<-eff_list$TranscriptID[eff_list$TranscriptID %in% sig$target_id[sig$change=="culture"]]
plot_bootstrap(so,
target_id = culture_eff[1],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = culture_eff[5],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = culture_eff[7],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = culture_eff[3],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = culture_eff[2],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = culture_eff[4],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = culture_eff[6],
units = "est_counts",
color_by = "condition")
lichen_unique<-counts_tab %>% filter(XBC2>0,XBA1>0,XSA2_2>0,XSC1>0,XSE2>0,XBE1>0,XTA2>0,XSC2>0,
XSA2>0,XBA2>0,XBC1>0,XTA1>0,XSA1>0,XTC2>0,XTE2>0,XBE2>0,XMC2>0,
S_21XB1==0,KS21XB1==0,S_21XB3==0,S_42XB1==0,S_42XB2==0,S_42XB3==0,
KS48XB1==0,KS48XB2==0,KS48XB3==0,KS9XB1==0,KS9XB2==0,KS9XB3==0) %>%
pivot_longer(-target_id,names_to="sample",values_to="counts") %>%
filter(counts>0, sample !="MP_I",sample !="MP_II") %>% group_by(target_id) %>% summarise(avg_counts_lichen=mean(as.numeric(counts))) %>%
left_join(funannot, by=c("target_id"="TranscriptID")) %>%
select(-c(CDS.transcript,Translation,gDNA,mRNA))
lichen_unique %>%
kable(format = "html", col.names = colnames(lichen_unique)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | avg_counts_lichen | GeneID | Feature | Contig | Start | Stop | Strand | Name | Product | Alias.Synonyms | EC_number | BUSCO | PFAM | InterPro | EggNog | COG | GO.Terms | Secreted | Membrane | Protease | CAZyme | antiSMASH | Notes | ProtID | CAZyme_new | COG_new | EggNog_new | GO.Terms_new | InterPro_new | PFAM_new | Protease_new | Secreted_new | KO |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_001612-T1 | 46.99245 | XANPAGTX0501_001612 | mRNA | Xp_GTX0501_2 | 2002693 | 2003141 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_001612_T1_XANPAGTX0501_001612 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_002783-T1 | 18.68803 | XANPAGTX0501_002783 | mRNA | Xp_GTX0501_4 | 808460 | 808865 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_002783_T1_XANPAGTX0501_002783 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_003199-T1 | 20.17647 | XANPAGTX0501_003199 | mRNA | Xp_GTX0501_5 | 87909 | 89177 |
|
AIM6_3 | Altered inheritance of mitochondria protein 6 | NA | NA | NA | NA | IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily;IPR039559 Altered inheritance of mitochondria protein 6, PI-PLC-like catalytic domain | ENOG503NZFJ | S:(S) Function unknown | GO_function: GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA];GO_process: GO:0006629 - lipid metabolic process [Evidence IEA] | NA | NA | NA | NA | Cluster_2 | NA | XANPAGTX0501_003199_T1_XANPAGTX0501_003199 | NA | S:(S) Function unknown | ENOG503NZFJ | GO_function: GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA], GO_process: GO:0006629 - lipid metabolic process [Evidence IEA] | IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily, IPR039559 Altered inheritance of mitochondria protein 6, PI-PLC-like catalytic domain | NA | NA | NA | |
| XANPAGTX0501_006970-T1 | 48.17647 | XANPAGTX0501_006970 | mRNA | Xp_GTX0501_11 | 354394 | 354648 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_006970_T1_XANPAGTX0501_006970 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_006972-T1 | 74.64706 | XANPAGTX0501_006972 | mRNA | Xp_GTX0501_11 | 357523 | 357828 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_006972_T1_XANPAGTX0501_006972 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_008008-T1 | 58.88235 | XANPAGTX0501_008008 | mRNA | Xp_GTX0501_14 | 138465 | 139439 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_008008_T1_XANPAGTX0501_008008 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_008856-T1 | 94.82353 | XANPAGTX0501_008856 | mRNA | Xp_GTX0501_17 | 399345 | 400886 |
|
NA | hypothetical protein | NA | NA | NA | NA | IPR032675 Leucine-rich repeat domain superfamily | NA | NA | NA | NA | NA | NA | NA | Cluster_1 | NA | XANPAGTX0501_008856_T1_XANPAGTX0501_008856 | NA | NA | ENOG503P83U | GO_function: GO:0005515 - protein binding [Evidence IEA] | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily | NA | NA | NA | |
| XANPAGTX0501_009040-T1 | 57.41176 | XANPAGTX0501_009040 | mRNA | Xp_GTX0501_18 | 366441 | 366695 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_009040_T1_XANPAGTX0501_009040 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_009438-T1 | 963.88235 | XANPAGTX0501_009438 | mRNA | Xp_GTX0501_21 | 196714 | 197521 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_009438_T1_XANPAGTX0501_009438 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_009555-T1 | 1952.88235 | XANPAGTX0501_009555 | mRNA | Xp_GTX0501_22 | 191143 | 191546 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_009555_T1_XANPAGTX0501_009555 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_009582-T1 | 17.00000 | XANPAGTX0501_009582 | mRNA | Xp_GTX0501_22 | 265438 | 265938 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_009582_T1_XANPAGTX0501_009582 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_009957-T1 | 69.00000 | XANPAGTX0501_009957 | mRNA | Xp_GTX0501_27 | 408 | 679 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Cluster_1 | NA | XANPAGTX0501_009957_T1_XANPAGTX0501_009957 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_010684-T1 | 45.11765 | XANPAGTX0501_010684 | mRNA | Xp_GTX0501_46 | 20975 | 22156 |
|
NA | hypothetical protein | NA | NA | NA | PF00067 | IPR001128 Cytochrome P450;IPR002401 Cytochrome P450, E-class, group I;IPR017972 Cytochrome P450, conserved site;IPR036396 Cytochrome P450 superfamily | ENOG503NWJC | Q:(Q) Secondary metabolites biosynthesis, transport and catabolism | GO_function: GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA];GO_function: GO:0020037 - heme binding [Evidence IEA];GO_function: GO:0005506 - iron ion binding [Evidence IEA];GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | NA | NA | NA | NA | NA | NA | XANPAGTX0501_010684_T1_XANPAGTX0501_010684 | NA | Q:(Q) Secondary metabolites biosynthesis, transport and catabolism | ENOG503NWJC | GO_function: GO:0005506 - iron ion binding [Evidence IEA], GO_function: GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA], GO_function: GO:0020037 - heme binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR001128 Cytochrome P450, IPR002401 Cytochrome P450, E-class, group I, IPR017972 Cytochrome P450, conserved site, IPR036396 Cytochrome P450 superfamily | PF00067 | NA | NA |
act as scavengers in the cell, collecting “junk” proteins to deliver to a “waste processor,” called the SCF complex, to which they dock through their F-box domain. In the SCF complex, the junk proteins are marked with ubiquitin for “incineration” in the proteasome. F-box proteins do not act indiscriminately but recruit specific, often modified proteins to the SCF complex and in this way regulate the level of certain proteins in a cell. F-box proteins are found in all eukaryotes and display a large variety of functions. In fungi they are, for example, involved in control of the cell division cycle, glucose sensing, mitochondrial connectivity, and control of the circadian clock
plot_bootstrap(so,
target_id = "XANPAGTX0501_008856-T1",
units = "est_counts",
color_by = "condition")
culture_unique<-counts_tab %>% filter(XBC2==0,XBA1==0,XSA2_2==0,XSC1==0,XSE2==0,XBE1==0,XTA2==0,XSC2==0,
XSA2==0,XBA2==0,XBC1==0,XTA1==0,XSA1==0,XTC2==0,XTE2==0,XBE2==0,XMC2==0,
S_21XB1>0,KS21XB1>0,S_21XB3>0,S_42XB1>0,S_42XB2>0,S_42XB3>0,
KS48XB1>0,KS48XB2>0,KS48XB3>0,KS9XB1>0,KS9XB2>0,KS9XB3>0) %>% pivot_longer(-target_id,names_to="sample",values_to="counts") %>%
filter(counts>0, sample !="MP_I",sample !="MP_II") %>% group_by(target_id) %>% summarise(avg_counts_culture=mean(as.numeric(counts))) %>%
left_join(funannot, by=c("target_id"="TranscriptID")) %>%
select(-c(CDS.transcript,Translation,gDNA,mRNA))
culture_unique %>%
kable(format = "html", col.names = colnames(culture_unique)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | avg_counts_culture | GeneID | Feature | Contig | Start | Stop | Strand | Name | Product | Alias.Synonyms | EC_number | BUSCO | PFAM | InterPro | EggNog | COG | GO.Terms | Secreted | Membrane | Protease | CAZyme | antiSMASH | Notes | ProtID | CAZyme_new | COG_new | EggNog_new | GO.Terms_new | InterPro_new | PFAM_new | Protease_new | Secreted_new | KO |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_008359-T2 | 967.2169 | XANPAGTX0501_008359 | mRNA | Xp_GTX0501_15 | 271800 | 273051 |
|
NA | hypothetical protein | NA | NA | NA | PF03881 | IPR011009 Protein kinase-like domain superfamily;IPR016477 Fructosamine/Ketosamine-3-kinase | ENOG503P2EP | G:(G) Carbohydrate transport and metabolism | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_008359_T2_XANPAGTX0501_008359 | NA | G:(G) Carbohydrate transport and metabolism | ENOG503NZHR, ENOG503P2EP | NA | IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase | PF03881 | NA | NA |
plot_bootstrap(so,
target_id = "XANPAGTX0501_002103-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_002104-T1",
units = "est_counts",
color_by = "condition")
galpha<-funannot %>% filter(grepl("IPR001019",InterPro_new))
sig %>% filter(target_id %in% galpha$TranscriptID)
## # A tibble: 5 × 12
## target_id pval qval b se_b mean_obs var_obs tech_var sigma_sq
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 XANPAGTX050… 2.19e-14 3.18e-13 0.625 0.0819 8.08 0.130 0.000966 0.0323
## 2 XANPAGTX050… 6.74e- 9 4.96e- 8 0.582 0.100 7.59 0.153 0.000548 0.0702
## 3 XANPAGTX050… 4.12e- 4 1.26e- 3 0.491 0.139 7.97 0.192 0.00126 0.135
## 4 XANPAGTX050… 2.57e- 3 6.48e- 3 0.233 0.0771 7.46 0.0288 0.000600 0.0152
## 5 XANPAGTX050… 2.58e- 2 4.90e- 2 0.210 0.0941 7.16 0.0712 0.000799 0.0615
## # ℹ 3 more variables: smooth_sigma_sq <dbl>, final_sigma_sq <dbl>, change <chr>
../02_long_read_assemblies/notebook/09_lichen_specific_genes.htmlfunannot2<-read.delim2("../../02_long_read_assemblies/analysis_and_temp_files/09_ortho/lichen_enriched_ortho_in_xanpa.tsv",sep="\t")
png("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_lichen_enriched_all.png",res=300,width=2000,height=1500)
plot_transcript_heatmap(so, transcripts=funannot2$TranscriptID[funannot2$lichen_ortho==T],
cluster_transcripts=T,show_rownames=F,
clustering_callback = callback)
dev.off()
## pdf
## 4
knitr::include_graphics("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_lichen_enriched_all.png")
og_sig<-sig %>% filter(target_id %in% funannot2$TranscriptID[funannot2$lichen_ortho==T])
og_sig %>% group_by(change) %>% summarise(n=n())
## # A tibble: 3 × 2
## change n
## <chr> <int>
## 1 culture 97
## 2 lichen 264
## 3 low_logFC 374
png("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_lichen_enriched_dge.png",res=300,width=2000,height=1000)
plot_transcript_heatmap(so, transcripts=og_sig$target_id[og_sig$change!="low_logFC"],
cluster_transcripts=T,show_rownames=F,
clustering_callback = callback)
dev.off()
## pdf
## 4
knitr::include_graphics("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_lichen_enriched_dge.png")
og_eff<-eff_list %>% filter(change %in% c("lichen","culture"),TranscriptID %in% og_sig$target_id)
og_eff %>%
kable(format = "html", col.names = colnames(og_eff)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | Product | EC_number | PFAM_new | InterPro_new | EggNog_new | COG_new | GO.Terms_new | Protease_new | CAZyme_new | antiSMASH | KO | pval | qval | b | se_b | mean_obs | var_obs | tech_var | sigma_sq | smooth_sigma_sq | final_sigma_sq | change |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_000656-T1 | hypothetical protein | IPR000772 Ricin B, lectin domain, IPR035992 Ricin B-like lectins | 0e+00 | 0.0e+00 | -4.357565 | 0.4814432 | 5.901784 | 6.3427509 | 0.0164185 | 1.6140872 | 0.0998084 | 1.6140872 | lichen | |||||||||
| XANPAGTX0501_001856-T1 | hypothetical protein | IPR037176 Osmotin/thaumatin-like superfamily | ENOG503P50I | 0e+00 | 0.0e+00 | -3.823871 | 0.4267541 | 5.375941 | 4.9088637 | 0.0242365 | 1.2568772 | 0.1485279 | 1.2568772 | lichen | ||||||||
| XANPAGTX0501_002409-T1 | hypothetical protein | IPR001338 Hydrophobin | GO_component: GO:0009277 - fungal-type cell wall [Evidence IEA], GO_function: GO:0005199 - structural constituent of cell wall [Evidence IEA] | 0e+00 | 0.0e+00 | -4.088717 | 0.2304978 | 9.598187 | 4.5603784 | 0.0003597 | 0.3733771 | 0.0994788 | 0.3733771 | lichen | ||||||||
| XANPAGTX0501_005118-T1 | hypothetical protein | ENOG503PWV2, ENOG503PYSR | Cluster_1 | 0e+00 | 0.0e+00 | 5.651733 | 0.6707321 | 2.530043 | 11.0765183 | 0.0109173 | 3.1537666 | 0.9389202 | 3.1537666 | culture | ||||||||
| XANPAGTX0501_006142-T1 | hypothetical protein | 0e+00 | 0.0e+00 | -2.552912 | 0.1836978 | 6.016577 | 1.8662663 | 0.0052380 | 0.2321399 | 0.0918787 | 0.2321399 | lichen | ||||||||||
| XANPAGTX0501_006194-T1 | hypothetical protein | 3.2.1.78 | IPR036908 RlpA-like domain superfamily | ENOG503P7ES | O:(O) Posttranslational modification, protein turnover, chaperones | 0e+00 | 0.0e+00 | -1.466337 | 0.1233940 | 5.850548 | 0.6054853 | 0.0035018 | 0.0642183 | 0.1036059 | 0.1036059 | lichen | ||||||
| XANPAGTX0501_006245-T1 | hypothetical protein | 0e+00 | 0.0e+00 | -3.929116 | 0.4012715 | 4.223801 | 4.9707307 | 0.0580619 | 1.0746222 | 0.3750018 | 1.0746222 | lichen | ||||||||||
| XANPAGTX0501_006967-T1 | hypothetical protein | 0e+00 | 0.0e+00 | -1.686952 | 0.1629173 | 6.974185 | 0.8949974 | 0.0013260 | 0.1853835 | 0.0471902 | 0.1853835 | lichen | ||||||||||
| XANPAGTX0501_007280-T1 | hypothetical protein | 2e-07 | 1.2e-06 | -1.317948 | 0.2534485 | 5.708208 | 0.8721158 | 0.0044510 | 0.4474169 | 0.1150951 | 0.4474169 | lichen | ||||||||||
| XANPAGTX0501_009189-T1 | hypothetical protein | 0e+00 | 0.0e+00 | -4.014594 | 0.3923972 | 2.368268 | 4.8172641 | 0.0859581 | 0.7106675 | 0.9971806 | 0.9971806 | lichen | ||||||||||
| XANPAGTX0501_009311-T1 | hypothetical protein | PF05730 | IPR008427 Extracellular membrane protein, CFEM domain | 0e+00 | 0.0e+00 | -1.019264 | 0.1582712 | 7.042583 | 0.4309233 | 0.0010038 | 0.1752083 | 0.0457542 | 0.1752083 | lichen |
funannot2 %>% group_by(antiSMASH,Contig) %>% summarize(n=n()) %>% filter(!is.na(antiSMASH))
## `summarise()` has grouped output by 'antiSMASH'. You can override using the
## `.groups` argument.
## # A tibble: 59 × 3
## # Groups: antiSMASH [7]
## antiSMASH Contig n
## <chr> <chr> <int>
## 1 Cluster_1 Xp_GTX0501_1 39
## 2 Cluster_1 Xp_GTX0501_10 20
## 3 Cluster_1 Xp_GTX0501_11 15
## 4 Cluster_1 Xp_GTX0501_12 12
## 5 Cluster_1 Xp_GTX0501_13 24
## 6 Cluster_1 Xp_GTX0501_14 11
## 7 Cluster_1 Xp_GTX0501_15 18
## 8 Cluster_1 Xp_GTX0501_17 24
## 9 Cluster_1 Xp_GTX0501_2 41
## 10 Cluster_1 Xp_GTX0501_24 44
## # ℹ 49 more rows
sm_genes<-funannot2 %>% filter(!is.na(antiSMASH)) %>% mutate(cluster = paste0(Contig,"_",antiSMASH)) %>% select(-c(gDNA,mRNA,CDS.transcript,Translation,CAZyme,COG,EggNog,GO.Terms,InterPro,PFAM,Protease,Secreted))
sm_sig<-sig %>% filter(target_id %in% sm_genes$TranscriptID)
sm_sig %>% group_by(change) %>% summarise(n=n())
## # A tibble: 3 × 2
## change n
## <chr> <int>
## 1 culture 96
## 2 lichen 222
## 3 low_logFC 379
png("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_SM_dge.png",res=300,width=2000,height=1000)
plot_transcript_heatmap(so, transcripts=sm_sig$target_id[sm_sig$change!="low_logFC"],
cluster_transcripts=T,show_rownames=F,
clustering_callback = callback)
dev.off()
## pdf
## 4
knitr::include_graphics("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_SM_dge.png")
library(splitstackshape)
antismash<-read.delim2("../../02_long_read_assemblies/analysis_and_temp_files/06_annotate_lecanoro/GTX0501_pred/antismash/antismash_summary.txt")
#get a list of all genes in each cluster
antismash_gene_all<-antismash %>% mutate(start_num=as.numeric(gsub("^.*?_","",Start)),
end_num=as.numeric(gsub("^.*?_","",End))) %>%
mutate(gene_number=end_num-start_num+1) %>%
expandRows("gene_number", drop = FALSE) %>%
group_by(start_num,end_num) %>%
mutate(gene_num = seq(start_num[1],end_num[1],by = 1)) %>%
mutate(GeneID=ifelse(gene_num<1000,paste0("XANPAGTX0501_000",gene_num),
ifelse(gene_num<10000,paste0("XANPAGTX0501_00",gene_num),
paste0("XANPAGTX0501_0",gene_num)))) %>%
mutate(Core_gene = ifelse(GeneID==Core_gene1|GeneID==Core_gene2,T,F)) %>% ungroup %>%
select(GeneID,Cluster,Description,Core_gene)
#add transcriptomic results
summary_antismash_all<-antismash_gene_all %>% left_join(funannot2,relationship = "many-to-many") %>%
left_join(sig, by = c("TranscriptID"="target_id")) %>%
group_by(Cluster,change) %>% summarize(n=n()) %>%
pivot_wider(names_from=change,values_from=n,values_fill=0) %>%
left_join(antismash)
## Joining with `by = join_by(GeneID)`
## `summarise()` has grouped output by 'Cluster'. You can override using the
## `.groups` argument.
## Joining with `by = join_by(Cluster)`
summary_antismash_core<-antismash_gene_all %>% filter(Core_gene==T) %>%
left_join(funannot2,relationship = "many-to-many") %>%
left_join(sig, by = c("TranscriptID"="target_id")) %>%
mutate(change=ifelse(change %in% c("lichen","culture"),change,"Non-DGE")) %>%
group_by(Cluster) %>% mutate(Core_gene_status=paste(change,collapse=",")) %>%
select(Cluster,Core_gene_status) %>% distinct()
## Joining with `by = join_by(GeneID)`
summary_antismash_core %>% group_by(Core_gene_status) %>%summarize(n=n())
## # A tibble: 6 × 2
## Core_gene_status n
## <chr> <int>
## 1 Non-DGE 35
## 2 Non-DGE,Non-DGE 2
## 3 culture 6
## 4 culture,culture 1
## 5 lichen 14
## 6 lichen,Non-DGE 1
summary_antismash_all<-summary_antismash_all %>% left_join(summary_antismash_core)
## Joining with `by = join_by(Cluster)`
summary_antismash_all %>%
kable(format = "html", col.names = colnames(summary_antismash_all)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| Cluster | culture | lichen | low_logFC | NA | Description | Start | End | Core_gene1 | Core_gene2 | KnownClusterBlast_MIBIG | KnownClusterBlast_description | KnownClusterBlast_Similarity | KnownClusterBlast_includes_core | Core_gene_status |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Xp_GTX0501_10_Cluster_1 | 2 | 12 | 4 | 2 | NRPS-like | XANPAGTX0501_006291 | XANPAGTX0501_006310 | XANPAGTX0501_006297 | NA | Non-DGE | ||||
| Xp_GTX0501_10_Cluster_2 | 2 | 9 | 6 | 8 | T1PKS | XANPAGTX0501_006308 | XANPAGTX0501_006332 | XANPAGTX0501_006319 | BGC0002215 | HEx-pks23 polyketide<ca> | 0.22 | 1 | lichen | |
| Xp_GTX0501_10_Cluster_3 | 0 | 2 | 14 | 11 | NRPS-like | XANPAGTX0501_006344 | XANPAGTX0501_006369 | XANPAGTX0501_006358 | NA | Non-DGE | ||||
| Xp_GTX0501_10_Cluster_4 | 2 | 1 | 14 | 9 | T3PKS | XANPAGTX0501_006734 | XANPAGTX0501_006757 | XANPAGTX0501_006744 | NA | Non-DGE | ||||
| Xp_GTX0501_11_Cluster_1 | 3 | 2 | 2 | 7 | NRPS | XANPAGTX0501_006840 | XANPAGTX0501_006853 | XANPAGTX0501_006845 | BGC0002235 | ACE1 | 0.11 | 1 | lichen | |
| Xp_GTX0501_12_Cluster_1 | 1 | 4 | 2 | 5 | T1PKS | XANPAGTX0501_007263 | XANPAGTX0501_007274 | XANPAGTX0501_007266 | BGC0000146 | solanapyrone D | 0.33 | 1 | Non-DGE | |
| Xp_GTX0501_12_Cluster_2 | 0 | 9 | 12 | 11 | T1PKS | XANPAGTX0501_007334 | XANPAGTX0501_007363 | XANPAGTX0501_007346 | NA | Non-DGE,Non-DGE | ||||
| Xp_GTX0501_12_Cluster_3 | 3 | 1 | 4 | 5 | terpene | XANPAGTX0501_007388 | XANPAGTX0501_007400 | XANPAGTX0501_007395 | NA | Non-DGE | ||||
| Xp_GTX0501_13_Cluster_1 | 1 | 5 | 2 | 14 | NRPS-like | XANPAGTX0501_007869 | XANPAGTX0501_007889 | XANPAGTX0501_007880 | NA | Non-DGE | ||||
| Xp_GTX0501_14_Cluster_1 | 1 | 2 | 4 | 3 | terpene | XANPAGTX0501_007984 | XANPAGTX0501_007993 | XANPAGTX0501_007988 | NA | Non-DGE | ||||
| Xp_GTX0501_15_Cluster_1 | 1 | 7 | 8 | 3 | NRPS-like | XANPAGTX0501_008267 | XANPAGTX0501_008284 | XANPAGTX0501_008272 | NA | lichen | ||||
| Xp_GTX0501_17_Cluster_1 | 0 | 7 | 8 | 7 | T1PKS | XANPAGTX0501_008845 | XANPAGTX0501_008866 | XANPAGTX0501_008852 | BGC0000156 |
TAN-1612 biosynthetic gene cluster from |
0.6 | 1 | lichen | |
| Xp_GTX0501_1_Cluster_1 | 5 | 6 | 12 | 15 | fungal-RiPP-like | XANPAGTX0501_000667 | XANPAGTX0501_000702 | XANPAGTX0501_000685 | NA | lichen | ||||
| Xp_GTX0501_1_Cluster_2 | 1 | 7 | 4 | 14 | T1PKS | XANPAGTX0501_000912 | XANPAGTX0501_000937 | XANPAGTX0501_000926 | BGC0000146 | solanapyrone D | 0.5 | 0 | Non-DGE | |
| Xp_GTX0501_24_Cluster_1 | 10 | 10 | 7 | 17 | fungal-RiPP-like | XANPAGTX0501_009693 | XANPAGTX0501_009736 | XANPAGTX0501_009715 | XANPAGTX0501_009716 | NA | culture,culture | |||
| Xp_GTX0501_25_Cluster_1 | 0 | 2 | 4 | 11 | terpene | XANPAGTX0501_009858 | XANPAGTX0501_009874 | XANPAGTX0501_009866 | NA | Non-DGE | ||||
| Xp_GTX0501_27_Cluster_1 | 1 | 2 | 12 | 7 | NRPS-like | XANPAGTX0501_009956 | XANPAGTX0501_009977 | XANPAGTX0501_009964 | NA | Non-DGE | ||||
| Xp_GTX0501_2_Cluster_1 | 2 | 6 | 15 | 16 | fungal-RiPP-like | XANPAGTX0501_001046 | XANPAGTX0501_001083 | XANPAGTX0501_001064 | NA | lichen | ||||
| Xp_GTX0501_2_Cluster_2 | 1 | 3 | 10 | 14 | NRPS | XANPAGTX0501_001225 | XANPAGTX0501_001250 | XANPAGTX0501_001239 | NA | Non-DGE | ||||
| Xp_GTX0501_2_Cluster_3 | 1 | 1 | 8 | 14 | NRPS-like | XANPAGTX0501_001291 | XANPAGTX0501_001314 | XANPAGTX0501_001305 | NA | Non-DGE | ||||
| Xp_GTX0501_2_Cluster_4 | 0 | 0 | 7 | 6 | terpene | XANPAGTX0501_001616 | XANPAGTX0501_001628 | XANPAGTX0501_001622 | NA | Non-DGE | ||||
| Xp_GTX0501_2_Cluster_5 | 0 | 2 | 3 | 18 | T1PKS | XANPAGTX0501_001669 | XANPAGTX0501_001691 | XANPAGTX0501_001679 | NA | Non-DGE | ||||
| Xp_GTX0501_2_Cluster_6 | 0 | 0 | 5 | 19 | NRP-metallophore | XANPAGTX0501_001682 | XANPAGTX0501_001705 | XANPAGTX0501_001696 | XANPAGTX0501_001694 | NA | Non-DGE,Non-DGE | |||
| Xp_GTX0501_2_Cluster_7 | 0 | 0 | 5 | 16 | NRPS | XANPAGTX0501_001682 | XANPAGTX0501_001702 | XANPAGTX0501_001694 | NA | Non-DGE | ||||
| Xp_GTX0501_35_Cluster_1 | 6 | 3 | 3 | 9 | NRPS-like | XANPAGTX0501_010404 | XANPAGTX0501_010423 | XANPAGTX0501_010409 | NA | culture | ||||
| Xp_GTX0501_35_Cluster_2 | 2 | 8 | 4 | 9 | T1PKS | XANPAGTX0501_010418 | XANPAGTX0501_010440 | XANPAGTX0501_010430 | NA | lichen | ||||
| Xp_GTX0501_36_Cluster_1 | 2 | 4 | 9 | 11 | T1PKS | XANPAGTX0501_010449 | XANPAGTX0501_010474 | XANPAGTX0501_010464 | BGC0001242 | oxyjavanicin | 0.25 | 1 | Non-DGE | |
| Xp_GTX0501_3_Cluster_1 | 10 | 8 | 0 | 3 | NRPS | XANPAGTX0501_001961 | XANPAGTX0501_001981 | XANPAGTX0501_001972 | BGC0001741 | phyllostictine A/phyllostictine B | 0.5 | 1 | culture | |
| Xp_GTX0501_3_Cluster_2 | 10 | 6 | 0 | 4 | T1PKS | XANPAGTX0501_001963 | XANPAGTX0501_001982 | XANPAGTX0501_001973 | BGC0001741 | phyllostictine A/phyllostictine B | 0.5 | 1 | culture | |
| Xp_GTX0501_3_Cluster_3 | 0 | 7 | 1 | 6 | terpene | XANPAGTX0501_002180 | XANPAGTX0501_002193 | XANPAGTX0501_002188 | NA | Non-DGE | ||||
| Xp_GTX0501_41_Cluster_1 | 0 | 1 | 9 | 3 | NRPS-like | XANPAGTX0501_010609 | XANPAGTX0501_010621 | XANPAGTX0501_010621 | NA | lichen | ||||
| Xp_GTX0501_43_Cluster_1 | 0 | 4 | 4 | 16 | T1PKS | XANPAGTX0501_010622 | XANPAGTX0501_010644 | XANPAGTX0501_010632 | NA | Non-DGE | ||||
| Xp_GTX0501_48_Cluster_1 | 3 | 6 | 2 | 8 | NRPS-like | XANPAGTX0501_010686 | XANPAGTX0501_010704 | XANPAGTX0501_010692 | NA | culture | ||||
| Xp_GTX0501_4_Cluster_1 | 1 | 0 | 3 | 9 | terpene | XANPAGTX0501_002454 | XANPAGTX0501_002466 | XANPAGTX0501_002460 | NA | Non-DGE | ||||
| Xp_GTX0501_4_Cluster_2 | 0 | 6 | 15 | 12 | NRPS-like | XANPAGTX0501_002475 | XANPAGTX0501_002501 | XANPAGTX0501_002488 | NA | lichen | ||||
| Xp_GTX0501_4_Cluster_3 | 0 | 1 | 6 | 7 | terpene | XANPAGTX0501_002520 | XANPAGTX0501_002531 | XANPAGTX0501_002527 | BGC0001839 | squalestatin S1 | 0.4 | 1 | Non-DGE | |
| Xp_GTX0501_4_Cluster_4 | 0 | 3 | 10 | 13 | NRPS | XANPAGTX0501_002525 | XANPAGTX0501_002549 | XANPAGTX0501_002535 | BGC0002164 | peramine | 1 | 1 | lichen | |
| Xp_GTX0501_4_Cluster_5 | 0 | 3 | 5 | 17 | NRPS | XANPAGTX0501_003108 | XANPAGTX0501_003131 | XANPAGTX0501_003119 | NA | lichen | ||||
| Xp_GTX0501_50_Cluster_1 | 0 | 2 | 1 | 3 | T1PKS | XANPAGTX0501_010705 | XANPAGTX0501_010710 | XANPAGTX0501_010709 | BGC0000146 | solanapyrone D | 0.33 | 1 | Non-DGE | |
| Xp_GTX0501_52_Cluster_1 | 2 | 3 | 1 | 2 | NRPS | XANPAGTX0501_010711 | XANPAGTX0501_010717 | XANPAGTX0501_010715 | NA | Non-DGE | ||||
| Xp_GTX0501_5_Cluster_1 | 4 | 5 | 2 | 9 | T1PKS | XANPAGTX0501_003170 | XANPAGTX0501_003189 | XANPAGTX0501_003176 | BGC0002515 | solanapyrone A | 0.4 | 1 | culture | |
| Xp_GTX0501_5_Cluster_2 | 7 | 5 | 7 | 7 | T1PKS | XANPAGTX0501_003179 | XANPAGTX0501_003204 | XANPAGTX0501_003194 | NA | Non-DGE | ||||
| Xp_GTX0501_5_Cluster_3 | 0 | 3 | 7 | 16 | NRPS,T1PKS | XANPAGTX0501_003287 | XANPAGTX0501_003311 | XANPAGTX0501_003300 | BGC0001067 | fumagillin/_-trans-bergamotene/fumagillol | 0.2 | 0 | Non-DGE | |
| Xp_GTX0501_5_Cluster_4 | 2 | 2 | 11 | 13 | NRPS-like | XANPAGTX0501_003361 | XANPAGTX0501_003388 | XANPAGTX0501_003374 | NA | lichen | ||||
| Xp_GTX0501_6_Cluster_1 | 0 | 3 | 10 | 10 | T1PKS | XANPAGTX0501_004370 | XANPAGTX0501_004390 | XANPAGTX0501_004380 | NA | Non-DGE | ||||
| Xp_GTX0501_6_Cluster_2 | 0 | 4 | 7 | 13 | T1PKS | XANPAGTX0501_004397 | XANPAGTX0501_004420 | XANPAGTX0501_004410 | NA | Non-DGE | ||||
| Xp_GTX0501_7_Cluster_1 | 0 | 4 | 10 | 12 | T1PKS | XANPAGTX0501_004611 | XANPAGTX0501_004634 | XANPAGTX0501_004622 | BGC0001258 | 1,3,6,8-tetrahydroxynaphthalene | 1 | 1 | Non-DGE | |
| Xp_GTX0501_7_Cluster_2 | 0 | 2 | 7 | 3 | terpene | XANPAGTX0501_004765 | XANPAGTX0501_004776 | XANPAGTX0501_004770 | NA | lichen | ||||
| Xp_GTX0501_7_Cluster_3 | 1 | 9 | 9 | 13 | T1PKS | XANPAGTX0501_005055 | XANPAGTX0501_005086 | XANPAGTX0501_005070 | NA | Non-DGE | ||||
| Xp_GTX0501_7_Cluster_4 | 1 | 7 | 7 | 10 | NRPS-like | XANPAGTX0501_005071 | XANPAGTX0501_005095 | XANPAGTX0501_005087 | NA | Non-DGE | ||||
| Xp_GTX0501_7_Cluster_5 | 1 | 8 | 7 | 8 | T1PKS | XANPAGTX0501_005075 | XANPAGTX0501_005098 | XANPAGTX0501_005090 | NA | Non-DGE | ||||
| Xp_GTX0501_8_Cluster_1 | 9 | 0 | 4 | 11 | NRPS | XANPAGTX0501_005105 | XANPAGTX0501_005128 | XANPAGTX0501_005116 | NA | culture | ||||
| Xp_GTX0501_8_Cluster_2 | 1 | 6 | 9 | 13 | T1PKS | XANPAGTX0501_005240 | XANPAGTX0501_005265 | XANPAGTX0501_005252 | NA | lichen | ||||
| Xp_GTX0501_8_Cluster_3 | 1 | 5 | 10 | 13 | T1PKS | XANPAGTX0501_005280 | XANPAGTX0501_005306 | XANPAGTX0501_005291 | BGC0000046 | depudecin | 0.33 | 0 | Non-DGE | |
| Xp_GTX0501_8_Cluster_4 | 5 | 4 | 11 | 15 | fungal-RiPP-like | XANPAGTX0501_005329 | XANPAGTX0501_005361 | XANPAGTX0501_005349 | NA | Non-DGE | ||||
| Xp_GTX0501_8_Cluster_5 | 1 | 3 | 4 | 5 | terpene | XANPAGTX0501_005377 | XANPAGTX0501_005388 | XANPAGTX0501_005382 | NA | lichen,Non-DGE | ||||
| Xp_GTX0501_9_Cluster_1 | 0 | 4 | 3 | 14 | T1PKS | XANPAGTX0501_005732 | XANPAGTX0501_005752 | XANPAGTX0501_005742 | BGC0001258 | 1,3,6,8-tetrahydroxynaphthalene | 1 | 1 | Non-DGE | |
| Xp_GTX0501_9_Cluster_2 | 2 | 0 | 5 | 16 | NRPS | XANPAGTX0501_005742 | XANPAGTX0501_005764 | XANPAGTX0501_005751 | NA | Non-DGE | ||||
| Xp_GTX0501_9_Cluster_3 | 2 | 3 | 12 | 11 | T1PKS | XANPAGTX0501_005922 | XANPAGTX0501_005948 | XANPAGTX0501_005935 | BGC0002194 | epipyrone A | 0.75 | 1 | Non-DGE |
summary_antismash_all %>% filter(culture==0,lichen>0,grepl("lichen",Core_gene_status)) %>%
kable(format = "html", col.names = colnames(summary_antismash_all)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| Cluster | culture | lichen | low_logFC | NA | Description | Start | End | Core_gene1 | Core_gene2 | KnownClusterBlast_MIBIG | KnownClusterBlast_description | KnownClusterBlast_Similarity | KnownClusterBlast_includes_core | Core_gene_status |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Xp_GTX0501_17_Cluster_1 | 0 | 7 | 8 | 7 | T1PKS | XANPAGTX0501_008845 | XANPAGTX0501_008866 | XANPAGTX0501_008852 | BGC0000156 |
TAN-1612 biosynthetic gene cluster from |
0.6 | 1 | lichen | |
| Xp_GTX0501_41_Cluster_1 | 0 | 1 | 9 | 3 | NRPS-like | XANPAGTX0501_010609 | XANPAGTX0501_010621 | XANPAGTX0501_010621 | NA | lichen | ||||
| Xp_GTX0501_4_Cluster_2 | 0 | 6 | 15 | 12 | NRPS-like | XANPAGTX0501_002475 | XANPAGTX0501_002501 | XANPAGTX0501_002488 | NA | lichen | ||||
| Xp_GTX0501_4_Cluster_4 | 0 | 3 | 10 | 13 | NRPS | XANPAGTX0501_002525 | XANPAGTX0501_002549 | XANPAGTX0501_002535 | BGC0002164 | peramine | 1 | 1 | lichen | |
| Xp_GTX0501_4_Cluster_5 | 0 | 3 | 5 | 17 | NRPS | XANPAGTX0501_003108 | XANPAGTX0501_003131 | XANPAGTX0501_003119 | NA | lichen | ||||
| Xp_GTX0501_7_Cluster_2 | 0 | 2 | 7 | 3 | terpene | XANPAGTX0501_004765 | XANPAGTX0501_004776 | XANPAGTX0501_004770 | NA | lichen |
sig %>% filter(target_id %in% c("XANPAGTX0501_008850-T1","XANPAGTX0501_008851-T1","XANPAGTX0501_008852-T1","XANPAGTX0501_008853-T1")) %>% select(target_id,qval,b,change)
## # A tibble: 4 × 4
## target_id qval b change
## <chr> <dbl> <dbl> <chr>
## 1 XANPAGTX0501_008850-T1 6.06e-22 -1.70 lichen
## 2 XANPAGTX0501_008851-T1 5.87e-21 -1.93 lichen
## 3 XANPAGTX0501_008852-T1 1.87e-22 -2.08 lichen
## 4 XANPAGTX0501_008853-T1 3.26e-69 -4.00 lichen
plot_bootstrap(so,
target_id = "XANPAGTX0501_008850-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_008851-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_008852-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_008853-T1",
units = "est_counts",
color_by = "condition")
funannot2 %>% filter(grepl("IPR000719",InterPro_new)) %>% group_by(lichen_ortho) %>% summarize(n=n())
## # A tibble: 2 × 2
## lichen_ortho n
## <lgl> <int>
## 1 FALSE 120
## 2 TRUE 24
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR000719",InterPro_new)) %>% group_by(change) %>% summarize(n=n())
## # A tibble: 4 × 2
## change n
## <chr> <int>
## 1 culture 12
## 2 lichen 13
## 3 low_logFC 55
## 4 <NA> 64
funannot2 %>% filter(grepl("IPR005828",InterPro_new)) %>% group_by(lichen_ortho) %>% summarize(n=n())
## # A tibble: 2 × 2
## lichen_ortho n
## <lgl> <int>
## 1 FALSE 33
## 2 TRUE 5
funannot2 %>% filter(grepl("IPR005828",InterPro_new),lichen_ortho==T) %>% select(TranscriptID,InterPro_new)
## TranscriptID
## 1 XANPAGTX0501_001653-T1
## 2 XANPAGTX0501_005571-T1
## 3 XANPAGTX0501_005572-T1
## 4 XANPAGTX0501_008617-T1
## 5 XANPAGTX0501_010000-T1
## InterPro_new
## 1 IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
## 2 IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
## 3 IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
## 4 IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
## 5 IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR005828",InterPro_new)) %>% group_by(change) %>% summarize(n=n())
## # A tibble: 4 × 2
## change n
## <chr> <int>
## 1 culture 2
## 2 lichen 6
## 3 low_logFC 16
## 4 <NA> 14
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR005828",InterPro_new),lichen_ortho==T) %>% group_by(change) %>% summarize(n=n())
## # A tibble: 2 × 2
## change n
## <chr> <int>
## 1 lichen 3
## 2 low_logFC 2
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR005828",InterPro_new),lichen_ortho==T) %>% select(TranscriptID,change,b,qval)
## TranscriptID change b qval
## 1 XANPAGTX0501_001653-T1 lichen -2.0408199 3.742386e-12
## 2 XANPAGTX0501_005571-T1 lichen -1.9797831 6.700776e-05
## 3 XANPAGTX0501_005572-T1 lichen -1.9025473 1.986579e-05
## 4 XANPAGTX0501_008617-T1 low_logFC -0.5728169 3.266494e-07
## 5 XANPAGTX0501_010000-T1 low_logFC -0.6135197 2.741270e-04
analysis_and_temp_files/08_dge_culture_lichen/blastp_polyol_transporters.txtsbatch --mem=5G -c 1 --wrap="source package d6092385-3a81-49d9-b044-8ffb85d0c446; blastp -query analysis_and_temp_files/08_dge_culture_lichen/polyol_transporters_genbank.fa -subject ../02_long_read_assemblies/analysis_and_temp_files/06_annotate_lecanoro/GTX0501_pred/annotate_results/Xanthoria_parietina_GTX0501.proteins.fa -outfmt 6 -out analysis_and_temp_files/08_dge_culture_lichen/blastp_polyol_transporters.txt -evalue 1e-100"
polyol_blast<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/blastp_polyol_transporters.txt",header=F)
polyol_blast<-polyol_blast %>% select(V1,V2,V11,V12)
colnames(polyol_blast)<-c("query","subject","e-value","score")
polyol_blast
## query subject e-value score
## 1 AAX98668.1 XANPAGTX0501_010000-T1 1.49e-179 516
## 2 AAX98668.1 XANPAGTX0501_001653-T1 5.32e-176 508
## 3 AAX98668.1 XANPAGTX0501_008617-T1 2.52e-114 350
## 4 CAR65543.1 XANPAGTX0501_005996-T1 0.0 602
## 5 CAR65543.1 XANPAGTX0501_007564-T1 9.63e-178 519
## 6 CAR65543.1 XANPAGTX0501_009339-T1 5.39e-151 449
## 7 CAR65543.1 XANPAGTX0501_009339-T2 2.57e-149 442
## 8 CAR65543.1 XANPAGTX0501_000906-T1 4.21e-145 434
## 9 CAR65543.1 XANPAGTX0501_001701-T1 7.68e-133 402
## 10 CAG86001.1 XANPAGTX0501_005996-T1 0.0 591
## 11 CAG86001.1 XANPAGTX0501_007564-T1 2.80e-178 520
## 12 CAG86001.1 XANPAGTX0501_009339-T1 1.51e-152 453
## 13 CAG86001.1 XANPAGTX0501_009339-T2 2.52e-150 445
## 14 CAG86001.1 XANPAGTX0501_000906-T1 3.81e-146 436
## 15 CAG86001.1 XANPAGTX0501_001701-T1 1.48e-132 401
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(TranscriptID %in% polyol_blast$subject) %>% select(TranscriptID,change,b,qval,lichen_ortho)
## TranscriptID change b qval lichen_ortho
## 1 XANPAGTX0501_000906-T1 <NA> NA NA FALSE
## 2 XANPAGTX0501_001653-T1 lichen -2.0408199 3.742386e-12 TRUE
## 3 XANPAGTX0501_001701-T1 low_logFC 0.6237851 2.869476e-06 FALSE
## 4 XANPAGTX0501_005996-T1 low_logFC 0.4003563 2.088997e-06 FALSE
## 5 XANPAGTX0501_007564-T1 low_logFC 0.2966283 4.581743e-02 FALSE
## 6 XANPAGTX0501_008617-T1 low_logFC -0.5728169 3.266494e-07 TRUE
## 7 XANPAGTX0501_009339-T1 <NA> NA NA FALSE
## 8 XANPAGTX0501_009339-T2 <NA> NA NA FALSE
## 9 XANPAGTX0501_010000-T1 low_logFC -0.6135197 2.741270e-04 TRUE
plot_bootstrap(so,
target_id = "XANPAGTX0501_001653-T1",
units = "est_counts",
color_by = "condition")
funannot2 %>% filter(grepl("IPR001905",InterPro_new)) %>% group_by(lichen_ortho) %>% summarize(n=n())
## # A tibble: 1 × 2
## lichen_ortho n
## <lgl> <int>
## 1 FALSE 2
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR001905",InterPro_new)) %>% select(TranscriptID,change,b,qval)
## TranscriptID change b qval
## 1 XANPAGTX0501_004972-T1 lichen -2.248389 3.681322e-56
## 2 XANPAGTX0501_009385-T1 <NA> NA NA
transport_lic<-funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("transport",InterPro_new),change=="lichen") %>% select(TranscriptID,InterPro_new,lichen_ortho)
transport_lic %>%
kable(format = "html", col.names = c("TranscriptID","InterPro_new","lichen_ortho")) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | InterPro_new | lichen_ortho |
|---|---|---|
| XANPAGTX0501_000142-T1 | IPR011701 Major facilitator superfamily, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_000342-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_000342-T2 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_000684-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_000704-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_001082-T1 | IPR004853 Sugar phosphate transporter domain | FALSE |
| XANPAGTX0501_001448-T1 | IPR011701 Major facilitator superfamily, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_001653-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_002486-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_003065-T3 | IPR005178 Organic solute transporter subunit alpha/Transmembrane protein 184 | FALSE |
| XANPAGTX0501_003337-T2 | IPR004738 Phosphate permease, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_004383-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_004428-T1 | IPR004695 Transporter protein SLAC1/Mae1/ Ssu1/TehA, IPR030185 Malic acid transport protein, IPR038665 Voltage-dependent anion channel superfamily | FALSE |
| XANPAGTX0501_004624-T1 | IPR004737 Nitrate transporter NarK/NarU-like, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_004972-T1 | IPR001905 Ammonium transporter, IPR018047 Ammonium transporter, conserved site, IPR024041 Ammonium transporter AmtB-like domain, IPR029020 Ammonium/urea transporter | FALSE |
| XANPAGTX0501_004996-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_005027-T1 | IPR003370 Chromate transporter, IPR014047 Chromate transporter, long chain | FALSE |
| XANPAGTX0501_005378-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_005489-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_005571-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_005572-T1 | IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_005708-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_006293-T1 | IPR001958 Tetracycline resistance protein TetA/multidrug resistance protein MdtG, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_006324-T1 | IPR001204 Phosphate transporter | FALSE |
| XANPAGTX0501_006367-T1 | IPR005829 Sugar transporter, conserved site, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_006527-T1 | IPR000791 Acetate transporter GPR1/FUN34/SatP family | FALSE |
| XANPAGTX0501_007882-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_007969-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_008850-T1 | IPR003439 ABC transporter-like, ATP-binding domain, IPR003593 AAA+ ATPase domain, IPR010929 CDR ABC transporter, IPR013525 ABC-2 type transporter, IPR017871 ABC transporter-like, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR029481 ABC-transporter, N-terminal domain, IPR034001 ATP-binding cassette transporter, PDR-like subfamily G, domain 1, IPR034003 ATP-binding cassette transporter, PDR-like subfamily G, domain 2 | FALSE |
| XANPAGTX0501_009192-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009193-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009202-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009320-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009472-T1 | IPR005018 DOMON domain, IPR006593 Cytochrome b561/ferric reductase transmembrane, IPR015920 Cellobiose dehydrogenase, cytochrome domain, IPR018825 Domain of unknown function DUF2427, IPR036259 MFS transporter superfamily, IPR038697 None | FALSE |
| XANPAGTX0501_009914-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_010175-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_010196-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_010381-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_010444-T1 | IPR001958 Tetracycline resistance protein TetA/multidrug resistance protein MdtG, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_010683-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_010706-T1 | IPR003439 ABC transporter-like, ATP-binding domain, IPR003593 AAA+ ATPase domain, IPR011527 ABC transporter type 1, transmembrane domain, IPR017871 ABC transporter-like, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR036640 ABC transporter type 1, transmembrane domain superfamily | FALSE |
transport_cul<-funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("transport",InterPro_new),change=="culture") %>% select(TranscriptID,InterPro_new,lichen_ortho)
transport_lic %>%
kable(format = "html", col.names = c("TranscriptID","InterPro_new","lichen_ortho")) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | InterPro_new | lichen_ortho |
|---|---|---|
| XANPAGTX0501_000142-T1 | IPR011701 Major facilitator superfamily, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_000342-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_000342-T2 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_000684-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_000704-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_001082-T1 | IPR004853 Sugar phosphate transporter domain | FALSE |
| XANPAGTX0501_001448-T1 | IPR011701 Major facilitator superfamily, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_001653-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_002486-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_003065-T3 | IPR005178 Organic solute transporter subunit alpha/Transmembrane protein 184 | FALSE |
| XANPAGTX0501_003337-T2 | IPR004738 Phosphate permease, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_004383-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_004428-T1 | IPR004695 Transporter protein SLAC1/Mae1/ Ssu1/TehA, IPR030185 Malic acid transport protein, IPR038665 Voltage-dependent anion channel superfamily | FALSE |
| XANPAGTX0501_004624-T1 | IPR004737 Nitrate transporter NarK/NarU-like, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_004972-T1 | IPR001905 Ammonium transporter, IPR018047 Ammonium transporter, conserved site, IPR024041 Ammonium transporter AmtB-like domain, IPR029020 Ammonium/urea transporter | FALSE |
| XANPAGTX0501_004996-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_005027-T1 | IPR003370 Chromate transporter, IPR014047 Chromate transporter, long chain | FALSE |
| XANPAGTX0501_005378-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_005489-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_005571-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_005572-T1 | IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_005708-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_006293-T1 | IPR001958 Tetracycline resistance protein TetA/multidrug resistance protein MdtG, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_006324-T1 | IPR001204 Phosphate transporter | FALSE |
| XANPAGTX0501_006367-T1 | IPR005829 Sugar transporter, conserved site, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_006527-T1 | IPR000791 Acetate transporter GPR1/FUN34/SatP family | FALSE |
| XANPAGTX0501_007882-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_007969-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_008850-T1 | IPR003439 ABC transporter-like, ATP-binding domain, IPR003593 AAA+ ATPase domain, IPR010929 CDR ABC transporter, IPR013525 ABC-2 type transporter, IPR017871 ABC transporter-like, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR029481 ABC-transporter, N-terminal domain, IPR034001 ATP-binding cassette transporter, PDR-like subfamily G, domain 1, IPR034003 ATP-binding cassette transporter, PDR-like subfamily G, domain 2 | FALSE |
| XANPAGTX0501_009192-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009193-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009202-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009320-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009472-T1 | IPR005018 DOMON domain, IPR006593 Cytochrome b561/ferric reductase transmembrane, IPR015920 Cellobiose dehydrogenase, cytochrome domain, IPR018825 Domain of unknown function DUF2427, IPR036259 MFS transporter superfamily, IPR038697 None | FALSE |
| XANPAGTX0501_009914-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_010175-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_010196-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_010381-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_010444-T1 | IPR001958 Tetracycline resistance protein TetA/multidrug resistance protein MdtG, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_010683-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_010706-T1 | IPR003439 ABC transporter-like, ATP-binding domain, IPR003593 AAA+ ATPase domain, IPR011527 ABC transporter type 1, transmembrane domain, IPR017871 ABC transporter-like, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR036640 ABC transporter type 1, transmembrane domain superfamily | FALSE |
secreted<-read.delim2("../../10_lichen_effectors/analysis_and_temp_files/01_predicting_effectors/all_secreted_list.txt",header=F)
secreted$TranscriptID<-str_replace(secreted$V1,"FUN","XANPAGTX0501")
png("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_secreted_all.png",res=300,width=2000,height=1500)
plot_transcript_heatmap(so, transcripts=secreted$TranscriptID,
cluster_transcripts=T,show_rownames=F,
clustering_callback = callback)
dev.off()
## pdf
## 4
knitr::include_graphics("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_secreted_all.png")
secreted_sig<-sig %>% filter(target_id %in% secreted$TranscriptID)
secreted_sig %>% group_by(change) %>% summarise(n=n())
## # A tibble: 3 × 2
## change n
## <chr> <int>
## 1 culture 40
## 2 lichen 154
## 3 low_logFC 192
secreted<-read.delim2("../../10_lichen_effectors/analysis_and_temp_files/01_predicting_effectors/all_secreted_list.txt",header=F)
secreted$TranscriptID<-str_replace(secreted$V1,"FUN","XANPAGTX0501")
png("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_secreted_dge.png",res=300,width=2000,height=1500)
plot_transcript_heatmap(so, transcripts=secreted_sig$target_id[secreted_sig$change!="low_logFC"],
cluster_transcripts=T,show_rownames=F,
clustering_callback = callback)
dev.off()
## pdf
## 4
knitr::include_graphics("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_secreted_dge.png")
secreted_table_lichen<-secreted_sig %>%
filter(change=="lichen") %>% left_join(funannot2,by = c("target_id"="TranscriptID")) %>% select(target_id,b,Product,CAZyme_new,COG_new,EggNog_new,GO.Terms_new,InterPro_new,PFAM_new,Protease_new,KO,lichen_ortho) %>% mutate(effector_from_small_list=ifelse(target_id %in% eff_list$TranscriptID,T,F))%>%
arrange(b)
secreted_table_lichen %>%
kable(format = "html", col.names = colnames(secreted_table_lichen)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | b | Product | CAZyme_new | COG_new | EggNog_new | GO.Terms_new | InterPro_new | PFAM_new | Protease_new | KO | lichen_ortho | effector_from_small_list |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_001127-T1 | -6.214566 | hypothetical protein | GH128 | NA | NA | NA | IPR008979 Galactose-binding-like domain superfamily, IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain | PF11790 | NA | FALSE | FALSE | |
| XANPAGTX0501_000655-T1 | -6.186697 | hypothetical protein | NA | NA | NA | NA | IPR035992 Ricin B-like lectins | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009887-T1 | -6.152645 | hypothetical protein | NA | NA | ENOG503P63W | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007865-T1 | -5.732812 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005533-T1 | -5.599048 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_010170-T1 | -5.061039 | hypothetical protein | NA | NA | NA | NA | IPR000772 Ricin B, lectin domain, IPR035992 Ricin B-like lectins | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_001063-T1 | -4.589396 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_009135-T1 | -4.527295 | hypothetical protein | NA | NA | NA | GO_component: GO:0005576 - extracellular region [Evidence IEA], GO_process: GO:0009405 - pathogenesis [Evidence IEA] | IPR011329 Killer toxin Kp4/SMK, IPR015131 Killer toxin, Kp4 | PF09044 | NA | FALSE | FALSE | |
| XANPAGTX0501_005364-T1 | -4.400832 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000656-T1 | -4.357565 | hypothetical protein | NA | NA | NA | NA | IPR000772 Ricin B, lectin domain, IPR035992 Ricin B-like lectins | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_002409-T1 | -4.088717 | hypothetical protein | NA | NA | NA | GO_component: GO:0009277 - fungal-type cell wall [Evidence IEA], GO_function: GO:0005199 - structural constituent of cell wall [Evidence IEA] | IPR001338 Hydrophobin | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_009189-T1 | -4.014594 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_001935-T1 | -3.959675 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006245-T1 | -3.929116 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_005061-T1 | -3.850853 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NVBA | NA | NA | PF13668 | NA | FALSE | FALSE | |
| XANPAGTX0501_001856-T1 | -3.823871 | hypothetical protein | NA | NA | ENOG503P50I | NA | IPR037176 Osmotin/thaumatin-like superfamily | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_006282-T1 | -3.776836 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004309-T1 | -3.720276 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004881-T1 | -3.693406 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001015-T1 | -3.506517 | hypothetical protein | NA | S:(S) Function unknown | ENOG503P58T, ENOG503P74E, ENOG503P76M | GO_process: GO:0042742 - defense response to bacterium [Evidence IEA], GO_process: GO:0050832 - defense response to fungus [Evidence IEA] | IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily | PF00967, PF03330 | NA | FALSE | TRUE | |
| XANPAGTX0501_010044-T1 | -3.501860 | hypothetical protein | NA | Q:(Q) Secondary metabolites biosynthesis, transport and catabolism | ENOG503NTXA | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR002937 Amine oxidase, IPR036188 FAD/NAD(P)-binding domain superfamily | PF13450 | NA | FALSE | FALSE | |
| XANPAGTX0501_009317-T1 | -3.484947 | hypothetical protein | NA | NA | NA | NA | IPR008979 Galactose-binding-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009340-T1 | -3.459083 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006327-T1 | -3.436352 | hypothetical protein | NA | NA | NA | NA | IPR018466 Yeast cell wall synthesis Kre9/Knh1-like, N-terminal | PF10342 | NA | FALSE | FALSE | |
| XANPAGTX0501_004930-T1 | -3.341143 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002446-T1 | -3.286528 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003765-T1 | -3.256318 | hypothetical protein | NA | NA | NA | GO_component: GO:0005618 - cell wall [Evidence IEA], GO_function: GO:0005199 - structural constituent of cell wall [Evidence IEA] | IPR000420 Yeast PIR protein repeat | PF00399 | NA | FALSE | FALSE | |
| XANPAGTX0501_005256-T1 | -3.224319 | hypothetical protein | AA7 | C:(C) Energy production and conversion | ENOG503NV4F | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_function: GO:0071949 - FAD binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR006094 FAD linked oxidase, N-terminal, IPR012951 Berberine/berberine-like, IPR016166 FAD-binding domain, PCMH-type, IPR036318 FAD-binding, type PCMH-like superfamily | PF01565, PF08031 | NA | TRUE | FALSE | |
| XANPAGTX0501_006846-T1 | -3.098928 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010449-T1 | -2.870515 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503P0GD | GO_function: GO:0004222 - metalloendopeptidase activity [Evidence IEA], GO_function: GO:0008237 - metallopeptidase activity [Evidence IEA], GO_process: GO:0006508 - proteolysis [Evidence IEA] | IPR001384 Peptidase M35, deuterolysin, IPR024079 Metallopeptidase, catalytic domain superfamily, IPR029463 Lysine-specific metallo-endopeptidase | PF02102, PF14521 | M35 | FALSE | FALSE | |
| XANPAGTX0501_009688-T1 | -2.868656 | hypothetical protein | NA | NA | NA | GO_component: GO:0005576 - extracellular region [Evidence IEA], GO_function: GO:0030248 - cellulose binding [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR000254 Cellulose-binding domain, fungal, IPR035971 Cellulose-binding domain superfamily, IPR036908 RlpA-like domain superfamily | PF00734 | NA | FALSE | TRUE | |
| XANPAGTX0501_003270-T1 | -2.857225 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004956-T1 | -2.837976 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005675-T1 | -2.825087 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NZAM | GO_function: GO:0008237 - metallopeptidase activity [Evidence IEA] | IPR008754 Peptidase M43, pregnancy-associated plasma-A, IPR024079 Metallopeptidase, catalytic domain superfamily | PF05572, PF13688 | M43B | FALSE | TRUE | |
| XANPAGTX0501_000163-T1 | -2.730902 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NXZU | NA | IPR009078 Ferritin-like superfamily | PF13668 | NA | TRUE | FALSE | |
| XANPAGTX0501_009886-T1 | -2.690801 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_009668-T1 | -2.648950 | hypothetical protein | NA | NA | ENOG503P6EY | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001304-T1 | -2.616995 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006142-T1 | -2.552912 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_003572-T1 | -2.535693 | hypothetical protein | CE16 | S:(S) Function unknown | ENOG503P02M | GO_function: GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA] | IPR001087 GDSL lipase/esterase, IPR036514 SGNH hydrolase superfamily | PF00657 | NA | FALSE | FALSE | |
| XANPAGTX0501_009606-T1 | -2.529422 | hypothetical protein | NA | NA | ENOG503PMNB | NA | IPR011024 Gamma-crystallin-like | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006291-T1 | -2.524612 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_008978-T1 | -2.518736 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005573-T1 | -2.506069 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_001458-T1 | -2.475919 | hypothetical protein | NA | G:(G) Carbohydrate transport and metabolism, O:(O) Posttranslational modification, protein turnover, chaperones, S:(S) Function unknown | ENOG503NVEA, ENOG503P073 | NA | IPR002889 Carbohydrate-binding WSC, IPR018535 Domain of unknown function DUF1996 | PF01822, PF09362 | NA | FALSE | FALSE | |
| XANPAGTX0501_005361-T1 | -2.474153 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007976-T1 | -2.346686 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009683-T1 | -2.345949 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005733-T1 | -2.302949 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_010693-T1 | -2.297042 | hypothetical protein | AA7 | C:(C) Energy production and conversion | ENOG503NVX6 | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_function: GO:0071949 - FAD binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR006094 FAD linked oxidase, N-terminal, IPR016166 FAD-binding domain, PCMH-type, IPR016167 FAD-binding, type PCMH, subdomain 1, IPR016169 FAD-binding, type PCMH, subdomain 2, IPR036318 FAD-binding, type PCMH-like superfamily | PF01565 | NA | TRUE | FALSE | |
| XANPAGTX0501_007272-T1 | -2.264531 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002412-T1 | -2.245791 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010247-T1 | -2.240976 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_007515-T1 | -2.210135 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NUDE, ENOG503NV31 | GO_function: GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA], GO_process: GO:0006508 - proteolysis [Evidence IEA] | IPR001461 Aspartic peptidase A1 family, IPR001969 Aspartic peptidase, active site, IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain, IPR034163 Aspergillopepsin-like catalytic domain | PF00026 | A01A | FALSE | FALSE | |
| XANPAGTX0501_005771-T1 | -2.208725 | hypothetical protein | GH5 | G:(G) Carbohydrate transport and metabolism | ENOG503NYXZ | GO_function: GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR001547 Glycoside hydrolase, family 5, IPR017853 Glycoside hydrolase superfamily | PF00150 | NA | FALSE | FALSE | |
| XANPAGTX0501_007362-T1 | -2.200339 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010580-T1 | -2.189884 | hypothetical protein | NA | G:(G) Carbohydrate transport and metabolism | ENOG501RPBK | GO_function: GO:0005515 - protein binding [Evidence IEA] | IPR011048 Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR019405 Lactonase, 7-bladed beta propeller | PF10282 | NA | FALSE | FALSE | |
| XANPAGTX0501_004978-T1 | -2.183515 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001708-T1 | -2.176671 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_009730-T1 | -2.155593 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009615-T1 | -2.152340 | hypothetical protein | NA | NA | NA | NA | IPR035940 CAP superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003873-T1 | -2.109258 | hypothetical protein | GH25 | G:(G) Carbohydrate transport and metabolism | ENOG503P1T2 | GO_function: GO:0003796 - lysozyme activity [Evidence IEA], GO_process: GO:0009253 - peptidoglycan catabolic process [Evidence IEA], GO_process: GO:0016998 - cell wall macromolecule catabolic process [Evidence IEA] | IPR002053 Glycoside hydrolase, family 25, IPR017853 Glycoside hydrolase superfamily, IPR018077 Glycoside hydrolase, family 25 subgroup | PF01183 | NA | FALSE | FALSE | |
| XANPAGTX0501_004880-T1 | -2.100330 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002331-T1 | -2.094181 | hypothetical protein | GH5 | G:(G) Carbohydrate transport and metabolism | ENOG503NY10 | GO_function: GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR001547 Glycoside hydrolase, family 5, IPR017853 Glycoside hydrolase superfamily, IPR018087 Glycoside hydrolase, family 5, conserved site | PF00150 | NA | FALSE | FALSE | |
| XANPAGTX0501_007467-T1 | -2.047189 | hypothetical protein | CE3 | G:(G) Carbohydrate transport and metabolism, S:(S) Function unknown | ENOG503NXZG, ENOG503P4E6 | NA | IPR013830 SGNH hydrolase-type esterase domain, IPR036514 SGNH hydrolase superfamily | PF00657, PF13472, PF13517 | NA | FALSE | FALSE | |
| XANPAGTX0501_008041-T1 | -2.018648 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010250-T1 | -1.956382 | hypothetical protein | NA | NA | ENOG503P3M4 | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_004329-T1 | -1.953200 | hypothetical protein | NA | NA | NA | NA | IPR020915 Uncharacterised protein family UPF0311 | PF11578 | NA | TRUE | FALSE | |
| XANPAGTX0501_008875-T1 | -1.934027 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_009699-T1 | -1.923092 | hypothetical protein | GH16 | G:(G) Carbohydrate transport and metabolism, O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NZM7, ENOG503PDKW | GO_function: GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA], GO_function: GO:0008061 - chitin binding [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR000757 Glycoside hydrolase family 16, IPR001002 Chitin-binding, type 1, IPR008264 Beta-glucanase, IPR013320 Concanavalin A-like lectin/glucanase domain superfamily, IPR036861 Endochitinase-like superfamily | PF00722 | NA | FALSE | FALSE | |
| XANPAGTX0501_010470-T1 | -1.921148 | hypothetical protein | GH24 | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503P2E0, ENOG503P2RE | GO_function: GO:0003796 - lysozyme activity [Evidence IEA], GO_process: GO:0009253 - peptidoglycan catabolic process [Evidence IEA], GO_process: GO:0016998 - cell wall macromolecule catabolic process [Evidence IEA], GO_process: GO:0019076 - viral release from host cell [Evidence IEA], GO_process: GO:0019835 - cytolysis [Evidence IEA] | IPR002196 Glycoside hydrolase, family 24, IPR009045 Hedgehog signalling/DD-peptidase zinc-binding domain superfamily, IPR023346 Lysozyme-like domain superfamily, IPR033907 Endolysin/autolysin, IPR034690 Endolysin T4 type | PF00959 | NA | K01185 | FALSE | TRUE |
| XANPAGTX0501_000609-T1 | -1.909619 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_006349-T1 | -1.876403 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000051-T1 | -1.859342 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_002665-T1 | -1.843112 | hypothetical protein | NA | NA | NA | GO_function: GO:0008237 - metallopeptidase activity [Evidence IEA] | IPR024079 Metallopeptidase, catalytic domain superfamily | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_001832-T1 | -1.829702 | hypothetical protein | GH128 | NA | NA | NA | IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain | PF11790 | NA | TRUE | FALSE | |
| XANPAGTX0501_004372-T1 | -1.826518 | hypothetical protein | NA | G:(G) Carbohydrate transport and metabolism, T:(T) Signal transduction mechanisms | ENOG503NV5A, ENOG503P0DZ | NA | IPR002018 Carboxylesterase, type B, IPR019819 Carboxylesterase type B, conserved site, IPR019826 Carboxylesterase type B, active site, IPR029058 Alpha/Beta hydrolase fold | PF00135, PF20434 | S09X | FALSE | FALSE | |
| XANPAGTX0501_010022-T1 | -1.809156 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000923-T1 | -1.786540 | hypothetical protein | NA | P:(P) Inorganic ion transport and metabolism | ENOG503NV06 | GO_function: GO:0003993 - acid phosphatase activity [Evidence IEA], GO_function: GO:0046872 - metal ion binding [Evidence IEA] | IPR008963 Purple acid phosphatase-like, N-terminal, IPR018946 PhoD-like phosphatase, metallophosphatase domain, IPR032093 Phospholipase D, N-terminal, IPR038607 PhoD-like superfamily | PF09423, PF16655 | NA | K01113 | FALSE | FALSE |
| XANPAGTX0501_003361-T1 | -1.748190 | hypothetical protein | NA | NA | ENOG503P519 | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009511-T1 | -1.745629 | hypothetical protein | GH16 | G:(G) Carbohydrate transport and metabolism, O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NZM7, ENOG503PDKW | GO_function: GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA], GO_function: GO:0008061 - chitin binding [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR000757 Glycoside hydrolase family 16, IPR001002 Chitin-binding, type 1, IPR008264 Beta-glucanase, IPR013320 Concanavalin A-like lectin/glucanase domain superfamily, IPR036861 Endochitinase-like superfamily | PF00722 | NA | K01216 | FALSE | FALSE |
| XANPAGTX0501_008019-T1 | -1.720017 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002191-T1 | -1.708273 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006967-T1 | -1.686952 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_005715-T1 | -1.646345 | hypothetical protein | AA7 | C:(C) Energy production and conversion, O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NXN6, ENOG503P15H | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_function: GO:0071949 - FAD binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR006094 FAD linked oxidase, N-terminal, IPR012951 Berberine/berberine-like, IPR016166 FAD-binding domain, PCMH-type, IPR036318 FAD-binding, type PCMH-like superfamily | PF01565, PF08031 | NA | FALSE | FALSE | |
| XANPAGTX0501_006283-T1 | -1.624636 | hypothetical protein | NA | NA | NA | NA | IPR000772 Ricin B, lectin domain, IPR035992 Ricin B-like lectins | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_008270-T1 | -1.619871 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005641-T1 | -1.614221 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_010366-T1 | -1.609971 | hypothetical protein | AA9 | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NYCR, ENOG503Q4YD | GO_function: GO:0003676 - nucleic acid binding [Evidence IEA], GO_function: GO:0008061 - chitin binding [Evidence IEA] | IPR001002 Chitin-binding, type 1, IPR005103 Auxiliary Activity family 9, IPR013087 Zinc finger C2H2-type, IPR018371 Chitin-binding, type 1, conserved site, IPR036861 Endochitinase-like superfamily | PF00187, PF03443 | NA | FALSE | FALSE | |
| XANPAGTX0501_000467-T1 | -1.600285 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_008622-T1 | -1.585245 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004346-T1 | -1.568986 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NUT8 | NA | IPR027589 Choice-of-anchor B domain | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006257-T1 | -1.562667 | hypothetical protein | NA | G:(G) Carbohydrate transport and metabolism | ENOG503NW21 | GO_function: GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR000490 Glycoside hydrolase family 17, IPR017853 Glycoside hydrolase superfamily | PF00332 | NA | K01210 | FALSE | FALSE |
| XANPAGTX0501_007939-T1 | -1.548201 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_010021-T1 | -1.539151 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009026-T1 | -1.512207 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_003287-T1 | -1.493602 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_002186-T1 | -1.483447 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006194-T1 | -1.466337 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503P7ES | NA | IPR036908 RlpA-like domain superfamily | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_004515-T1 | -1.449838 | hypothetical protein | NA | NA | NA | NA | IPR032710 NTF2-like domain superfamily, IPR037401 SnoaL-like domain | PF13577 | NA | FALSE | FALSE | |
| XANPAGTX0501_010040-T1 | -1.448217 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010027-T1 | -1.444367 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_009972-T1 | -1.430084 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503Q3UA | GO_function: GO:0004252 - serine-type endopeptidase activity [Evidence IEA], GO_function: GO:0008236 - serine-type peptidase activity [Evidence IEA], GO_process: GO:0006508 - proteolysis [Evidence IEA] | IPR000209 Peptidase S8/S53 domain, IPR015366 Peptidase S53, activation domain, IPR030400 Sedolisin domain, IPR036852 Peptidase S8/S53 domain superfamily | PF00082, PF09286 | S53 | TRUE | FALSE | |
| XANPAGTX0501_001919-T1 | -1.411388 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000162-T1 | -1.389788 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003766-T1 | -1.385254 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003448-T1 | -1.383005 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_009936-T1 | -1.379267 | hypothetical protein | AA5, CBM32 | O:(O) Posttranslational modification, protein turnover, chaperones, S:(S) Function unknown | ENOG502I4WM, ENOG503NY8H | GO_function: GO:0005515 - protein binding [Evidence IEA] | IPR000421 Coagulation factor 5/8 C-terminal domain, IPR006652 Kelch repeat type 1, IPR008979 Galactose-binding-like domain superfamily, IPR011043 Galactose oxidase/kelch, beta-propeller, IPR013783 Immunoglobulin-like fold, IPR014756 Immunoglobulin E-set, IPR015202 Galactose oxidase-like, Early set domain, IPR037293 Galactose oxidase, central domain superfamily | PF00754, PF01344, PF09118 | NA | FALSE | FALSE | |
| XANPAGTX0501_008146-T1 | -1.360688 | hypothetical protein | NA | E:(E) Amino acid transport and metabolism, O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503P41K | GO_function: GO:0004185 - serine-type carboxypeptidase activity [Evidence IEA], GO_process: GO:0006508 - proteolysis [Evidence IEA] | IPR001563 Peptidase S10, serine carboxypeptidase, IPR018202 Serine carboxypeptidase, serine active site, IPR029058 Alpha/Beta hydrolase fold | PF00450 | S10 | K01288 | FALSE | FALSE |
| XANPAGTX0501_010026-T1 | -1.349396 | hypothetical protein | NA | S:(S) Function unknown | ENOG503P0BZ | NA | IPR018392 LysM domain, IPR036779 LysM domain superfamily | PF01476 | NA | FALSE | FALSE | |
| XANPAGTX0501_001455-T1 | -1.338580 | Sperm-associated antigen 4 protein | GH132 | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NUJ1 | NA | IPR005556 SUN family | PF03856 | NA | K01238 | FALSE | FALSE |
| XANPAGTX0501_002315-T2 | -1.329521 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_009690-T1 | -1.325638 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_007280-T1 | -1.317948 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_004983-T1 | -1.308098 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005133-T1 | -1.291558 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NXPR | NA | IPR039535 Arylsulfotransferase-like | PF05935, PF14269 | NA | FALSE | FALSE | |
| XANPAGTX0501_000606-T1 | -1.268241 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007268-T1 | -1.263293 | hypothetical protein | AA7 | C:(C) Energy production and conversion, S:(S) Function unknown | ENOG503NXRX, ENOG503PBAU | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_function: GO:0071949 - FAD binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR006094 FAD linked oxidase, N-terminal, IPR012951 Berberine/berberine-like, IPR016166 FAD-binding domain, PCMH-type, IPR016167 FAD-binding, type PCMH, subdomain 1, IPR016169 FAD-binding, type PCMH, subdomain 2, IPR036318 FAD-binding, type PCMH-like superfamily | PF01565, PF08031 | NA | TRUE | FALSE | |
| XANPAGTX0501_004065-T1 | -1.250886 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006382-T1 | -1.241749 | hypothetical protein | NA | NA | ENOG503P53I | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005717-T1 | -1.235652 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008990-T1 | -1.228845 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009689-T1 | -1.216985 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009731-T1 | -1.215351 | hypothetical protein | GH71 | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NVTC | GO_function: GO:0016787 - hydrolase activity [Evidence IEA] | IPR005197 Glycoside hydrolase family 71 | PF03659 | NA | K08254 | FALSE | FALSE |
| XANPAGTX0501_008429-T1 | -1.195150 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_001183-T1 | -1.191723 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000737-T1 | -1.183761 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010624-T1 | -1.176356 | hypothetical protein | NA | J:(J) Translation, ribosomal structure and biogenesis | ENOG503NVR9 | NA | IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003606-T1 | -1.168749 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005629-T1 | -1.163876 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NY4Y | GO_function: GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA], GO_process: GO:0006629 - lipid metabolic process [Evidence IEA] | IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily, IPR030395 Glycerophosphodiester phosphodiesterase domain | PF03009 | NA | FALSE | FALSE | |
| XANPAGTX0501_002565-T1 | -1.159972 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006751-T1 | -1.137824 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010682-T1 | -1.134135 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_000697-T1 | -1.131109 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002041-T1 | -1.127546 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006292-T1 | -1.107115 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010443-T1 | -1.107115 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005317-T1 | -1.102348 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002543-T1 | -1.098046 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006860-T1 | -1.097166 | hypothetical protein | NA | NA | NA | NA | IPR008979 Galactose-binding-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007655-T1 | -1.094363 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NV1P | GO_function: GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA], GO_process: GO:0006629 - lipid metabolic process [Evidence IEA] | IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001970-T1 | -1.089366 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009607-T1 | -1.069439 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_010370-T1 | -1.066233 | hypothetical protein | NA | NA | NA | NA | IPR003609 PAN/Apple domain | PF00024 | NA | FALSE | FALSE | |
| XANPAGTX0501_002412-T2 | -1.065097 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003285-T1 | -1.064411 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NV2A | GO_function: GO:0008236 - serine-type peptidase activity [Evidence IEA], GO_process: GO:0006508 - proteolysis [Evidence IEA] | IPR008758 Peptidase S28, IPR029058 Alpha/Beta hydrolase fold, IPR042269 Serine carboxypeptidase S28, SKS domain | NA | S28 | K09649 | FALSE | FALSE |
| XANPAGTX0501_000434-T1 | -1.045784 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003186-T1 | -1.045733 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_009011-T1 | -1.036787 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_002514-T1 | -1.030316 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008683-T1 | -1.021294 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009311-T1 | -1.019264 | hypothetical protein | NA | NA | NA | NA | IPR008427 Extracellular membrane protein, CFEM domain | PF05730 | NA | TRUE | TRUE | |
| XANPAGTX0501_008027-T1 | -1.017996 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NZ6V | GO_function: GO:0004601 - peroxidase activity [Evidence IEA] | IPR000028 Chloroperoxidase, IPR036851 Chloroperoxidase-like superfamily | PF01328 | NA | FALSE | FALSE | |
| XANPAGTX0501_003124-T1 | -1.008637 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503P2G1 | GO_function: GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA], GO_process: GO:0006508 - proteolysis [Evidence IEA] | IPR001461 Aspartic peptidase A1 family, IPR001969 Aspartic peptidase, active site, IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain, IPR034164 Pepsin-like domain | PF00026 | A01A | FALSE | FALSE |
secreted_table_culture<-secreted_sig %>%
filter(change=="culture") %>% left_join(funannot2,by = c("target_id"="TranscriptID")) %>% select(target_id,b,Product,CAZyme_new,COG_new,EggNog_new,GO.Terms_new,InterPro_new,PFAM_new,Protease_new,KO,lichen_ortho) %>% mutate(effector_from_small_list=ifelse(target_id %in% eff_list$TranscriptID,T,F)) %>%
arrange(desc(b))
secreted_table_culture %>%
kable(format = "html", col.names = colnames(secreted_table_culture)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | b | Product | CAZyme_new | COG_new | EggNog_new | GO.Terms_new | InterPro_new | PFAM_new | Protease_new | KO | lichen_ortho | effector_from_small_list |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_005691-T1 | 5.859572 | hypothetical protein | AA7 | C:(C) Energy production and conversion | ENOG503NVX6 | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_function: GO:0071949 - FAD binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR006094 FAD linked oxidase, N-terminal, IPR016166 FAD-binding domain, PCMH-type, IPR016167 FAD-binding, type PCMH, subdomain 1, IPR016169 FAD-binding, type PCMH, subdomain 2, IPR036318 FAD-binding, type PCMH-like superfamily | PF01565 | NA | TRUE | FALSE | |
| XANPAGTX0501_005118-T1 | 5.651733 | hypothetical protein | NA | NA | ENOG503PWV2, ENOG503PYSR | NA | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_006848-T1 | 3.980717 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_008294-T1 | 3.732327 | hypothetical protein | AA5, CBM32 | O:(O) Posttranslational modification, protein turnover, chaperones, S:(S) Function unknown | ENOG502I4WM, ENOG503NY8H | GO_function: GO:0005515 - protein binding [Evidence IEA] | IPR000421 Coagulation factor 5/8 C-terminal domain, IPR006652 Kelch repeat type 1, IPR008979 Galactose-binding-like domain superfamily, IPR011043 Galactose oxidase/kelch, beta-propeller, IPR013783 Immunoglobulin-like fold, IPR014756 Immunoglobulin E-set, IPR015202 Galactose oxidase-like, Early set domain, IPR037293 Galactose oxidase, central domain superfamily | PF00754, PF01344, PF09118 | NA | FALSE | FALSE | |
| XANPAGTX0501_010474-T1 | 3.724444 | hypothetical protein | NA | NA | NA | NA | IPR008979 Galactose-binding-like domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_003863-T2 | 3.301034 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000306-T1 | 3.231592 | hypothetical protein | NA | S:(S) Function unknown | ENOG503P21A | NA | IPR021851 Protein of unknown function DUF3455 | PF11937 | NA | FALSE | FALSE | |
| XANPAGTX0501_006869-T1 | 3.075100 | hypothetical protein | GH128 | NA | NA | NA | IPR008979 Galactose-binding-like domain superfamily, IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain | PF11790 | NA | FALSE | FALSE | |
| XANPAGTX0501_005759-T1 | 2.880832 | hypothetical protein | NA | NA | ENOG503P558 | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009761-T1 | 2.701300 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NZQD | GO_component: GO:0005576 - extracellular region [Evidence IEA] | IPR001283 Cysteine-rich secretory protein-related, IPR014044 CAP domain, IPR018244 Allergen V5/Tpx-1-related, conserved site, IPR034120 None, IPR035940 CAP superfamily | PF00188 | NA | K20412 | FALSE | FALSE |
| XANPAGTX0501_000850-T1 | 2.534878 | hypothetical protein | NA | NA | ENOG503P7C3 | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006926-T1 | 2.528494 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_009613-T1 | 2.515673 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NZZ0 | NA | IPR000073 Alpha/beta hydrolase fold-1, IPR029058 Alpha/Beta hydrolase fold | PF12697 | NA | TRUE | FALSE | |
| XANPAGTX0501_010126-T2 | 2.407552 | hypothetical protein | NA | NA | NA | GO_function: GO:0008237 - metallopeptidase activity [Evidence IEA] | IPR024079 Metallopeptidase, catalytic domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009170-T1 | 2.253664 | hypothetical protein | GH45 | G:(G) Carbohydrate transport and metabolism | ENOG503P08U, ENOG503Q3X3 | GO_function: GO:0008810 - cellulase activity [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR000334 Glycoside hydrolase, family 45, IPR036908 RlpA-like domain superfamily | PF02015 | NA | FALSE | TRUE | |
| XANPAGTX0501_001974-T1 | 2.218747 | hypothetical protein | AA7 | C:(C) Energy production and conversion | ENOG503NWXH | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_function: GO:0071949 - FAD binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR006094 FAD linked oxidase, N-terminal, IPR012951 Berberine/berberine-like, IPR016166 FAD-binding domain, PCMH-type, IPR016167 FAD-binding, type PCMH, subdomain 1, IPR016169 FAD-binding, type PCMH, subdomain 2, IPR036318 FAD-binding, type PCMH-like superfamily | PF01565, PF08031 | NA | TRUE | FALSE | |
| XANPAGTX0501_010307-T1 | 1.956031 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003850-T1 | 1.889111 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009609-T1 | 1.620965 | hypothetical protein | NA | I:(I) Lipid transport and metabolism, S:(S) Function unknown | ENOG503NZ1V | GO_function: GO:0004806 - triglyceride lipase activity [Evidence IEA], GO_process: GO:0016042 - lipid catabolic process [Evidence IEA] | IPR000073 Alpha/beta hydrolase fold-1, IPR005152 Lipase, secreted, IPR022742 Serine aminopeptidase, S33, IPR029058 Alpha/Beta hydrolase fold | PF03583, PF12146, PF12697 | NA | TRUE | FALSE | |
| XANPAGTX0501_010442-T1 | 1.618450 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_005664-T1 | 1.551288 | hypothetical protein | GH128 | NA | NA | NA | IPR008979 Galactose-binding-like domain superfamily, IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain | PF11790 | NA | FALSE | FALSE | |
| XANPAGTX0501_007937-T1 | 1.503271 | hypothetical protein | NA | NA | ENOG503NVDR | GO_function: GO:0005515 - protein binding [Evidence IEA] | IPR011044 Quinoprotein amine dehydrogenase, beta chain-like, IPR015943 WD40/YVTN repeat-like-containing domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000401-T1 | 1.401801 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007985-T1 | 1.397612 | hypothetical protein | NA | NA | NA | GO_function: GO:0008237 - metallopeptidase activity [Evidence IEA] | IPR024079 Metallopeptidase, catalytic domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006091-T1 | 1.369228 | hypothetical protein | NA | NA | ENOG503P8K1 | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009962-T1 | 1.333092 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007182-T1 | 1.319524 | alpha,alpha-trehalase ath1 | NA | G:(G) Carbohydrate transport and metabolism | ENOG503NUMQ | GO_function: GO:0003824 - catalytic activity [Evidence IEA], GO_function: GO:0030246 - carbohydrate binding [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR005195 Glycoside hydrolase, family 65, central catalytic, IPR005196 Glycoside hydrolase, family 65, N-terminal, IPR008928 Six-hairpin glycosidase superfamily, IPR008979 Galactose-binding-like domain superfamily, IPR011013 Galactose mutarotase-like domain superfamily, IPR012341 Six-hairpin glycosidase-like superfamily, IPR037018 Glycoside hydrolase family 65, N-terminal domain superfamily | PF03633, PF03636 | NA | FALSE | FALSE | |
| XANPAGTX0501_010132-T1 | 1.308632 | hypothetical protein | GH43 | G:(G) Carbohydrate transport and metabolism | ENOG503P1F3 | GO_function: GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR006710 Glycoside hydrolase, family 43, IPR023296 Glycosyl hydrolase, five-bladed beta-propellor domain superfamily | PF04616 | NA | FALSE | FALSE | |
| XANPAGTX0501_005244-T1 | 1.304550 | hypothetical protein | AA3 | E:(E) Amino acid transport and metabolism | ENOG503NU6B, ENOG503NUFD | GO_function: GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal, IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal, IPR012132 Glucose-methanol-choline oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily | PF00732, PF05199 | NA | K00115 | FALSE | FALSE |
| XANPAGTX0501_007388-T1 | 1.269375 | hypothetical protein | NA | S:(S) Function unknown | ENOG503P3AN | GO_function: GO:0005515 - protein binding [Evidence IEA] | IPR002372 Pyrrolo-quinoline quinone repeat, IPR011047 Quinoprotein alcohol dehydrogenase-like superfamily, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006386-T1 | 1.206100 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002723-T1 | 1.203666 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NXPR | NA | IPR039535 Arylsulfotransferase-like | PF05935, PF14269 | NA | FALSE | FALSE | |
| XANPAGTX0501_006694-T1 | 1.155895 | hypothetical protein | NA | NA | ENOG503P24M | NA | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010191-T1 | 1.151281 | hypothetical protein | CE5 | G:(G) Carbohydrate transport and metabolism | ENOG503P4Q7 | GO_component: GO:0005576 - extracellular region [Evidence IEA], GO_function: GO:0016787 - hydrolase activity [Evidence IEA], GO_function: GO:0050525 - cutinase activity [Evidence IEA] | IPR000675 Cutinase/acetylxylan esterase, IPR011150 Cutinase, monofunctional, IPR029058 Alpha/Beta hydrolase fold | PF01083 | NA | FALSE | TRUE | |
| XANPAGTX0501_001051-T1 | 1.077085 | hypothetical protein | GH17 | G:(G) Carbohydrate transport and metabolism | ENOG503NXKT | NA | IPR017853 Glycoside hydrolase superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009124-T1 | 1.069091 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NVXI, ENOG503P4UQ | GO_component: GO:0005618 - cell wall [Evidence IEA], GO_function: GO:0005199 - structural constituent of cell wall [Evidence IEA] | IPR000420 Yeast PIR protein repeat | PF00399 | NA | FALSE | FALSE | |
| XANPAGTX0501_007482-T1 | 1.051174 | hypothetical protein | GH132 | S:(S) Function unknown | ENOG503NVKV | NA | IPR005556 SUN family | PF03856 | NA | FALSE | FALSE | |
| XANPAGTX0501_003140-T1 | 1.035102 | hypothetical protein | AA3 | E:(E) Amino acid transport and metabolism | ENOG503PBWU | GO_function: GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal, IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal, IPR012132 Glucose-methanol-choline oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily | PF00732, PF05199 | NA | TRUE | FALSE | |
| XANPAGTX0501_009902-T1 | 1.034038 | hypothetical protein | NA | P:(P) Inorganic ion transport and metabolism | ENOG503NY8E | NA | IPR001148 Alpha carbonic anhydrase domain, IPR036398 Alpha carbonic anhydrase domain superfamily, IPR041891 Carbonic anhydrase, prokaryotic-like | PF00194 | NA | K01672 | FALSE | FALSE |
| XANPAGTX0501_010393-T1 | 1.019087 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | FALSE |
nlr_list<-read.delim2("../../02_long_read_assemblies/analysis_and_temp_files/10_nlr/NLRs.txt")
nlr_sig<-sig %>% filter(target_id %in% nlr_list$TranscriptID)
nlr_sig %>% group_by(change) %>% summarise(n=n())
## # A tibble: 3 × 2
## change n
## <chr> <int>
## 1 culture 1
## 2 lichen 4
## 3 low_logFC 9
nlr_lichen<-nlr_sig$target_id[nlr_sig$change=="lichen"]
plot_bootstrap(so,
target_id = nlr_lichen[1],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = nlr_lichen[2],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = nlr_lichen[3],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = nlr_lichen[4],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = nlr_sig$target_id[nlr_sig$change=="culture"],
units = "est_counts",
color_by = "condition")
nlr_like<-read.delim2("../../02_long_read_assemblies/analysis_and_temp_files/10_nlr/NLR_like.txt")
nlrlike_sig<-sig %>% filter(target_id %in% nlr_like$TranscriptID) %>% arrange(b)
nlrlike_sig %>% group_by(change) %>% summarise(n=n())
## # A tibble: 3 × 2
## change n
## <chr> <int>
## 1 culture 3
## 2 lichen 12
## 3 low_logFC 14
plot_bootstrap(so,
target_id = nlrlike_sig$target_id[1],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = nlrlike_sig$target_id[2],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = nlrlike_sig$target_id[3],
units = "est_counts",
color_by = "condition")
funannot2 %>% filter(grepl("IPR038305",InterPro_new) |
grepl("IPR029498",InterPro_new) |
grepl("IPR010730",InterPro_new)) %>%
group_by(lichen_ortho) %>% summarize(n=n())
## # A tibble: 2 × 2
## lichen_ortho n
## <lgl> <int>
## 1 FALSE 57
## 2 TRUE 16
het_sig<-funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR038305",InterPro_new) |
grepl("IPR029498",InterPro_new) |
grepl("IPR010730",InterPro_new)) %>% arrange(b)
het_sig %>% group_by(change) %>% summarize(n=n())
## # A tibble: 4 × 2
## change n
## <chr> <int>
## 1 culture 6
## 2 lichen 14
## 3 low_logFC 24
## 4 <NA> 29
het_sig2<-het_sig %>% filter(!(TranscriptID %in% nlrlike_sig$target_id),!is.na(b))
het_sig2 %>% group_by(change) %>% summarize(n=n())
## # A tibble: 3 × 2
## change n
## <chr> <int>
## 1 culture 5
## 2 lichen 10
## 3 low_logFC 20
plot_bootstrap(so,
target_id = het_sig2$TranscriptID[1],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = het_sig2$TranscriptID[2],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = het_sig2$TranscriptID[3],
units = "est_counts",
color_by = "condition")
* Visualize most culture-upregulated * For first and third, expression in lichens is very non-uniform * Second looks more regular
plot_bootstrap(so,
target_id = het_sig2$TranscriptID[nrow(het_sig2)],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = het_sig2$TranscriptID[nrow(het_sig2)-1],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = het_sig2$TranscriptID[nrow(het_sig2)-2],
units = "est_counts",
color_by = "condition")
fbox<-sig2 %>% filter(grepl("F-box",InterPro_new),change!="low_logFC")
plot_bootstrap(so,
target_id = fbox$target_id[10],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = fbox$target_id[9],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = fbox$target_id[4],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = fbox$target_id[5],
units = "est_counts",
color_by = "condition")
poz<-sig2 %>% filter(grepl("BTB/POZ",InterPro_new),change!="low_logFC")
plot_bootstrap(so,
target_id = poz$target_id[3],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_002123-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_003775-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_008184-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_001825-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_009737-T1",
units = "est_counts",
color_by = "condition")
#make color mapping consistent between different heatmaps
library(circlize)
library(extrafont)
col_fun <- colorRamp2(seq(0,8,length.out = 100), viridis(100))
filt_mat<-subset(trans_mat, rownames(trans_mat) %in% annotation$TranscriptID)
HM_all = Heatmap(filt_mat, show_row_names = F, show_column_names = T, row_title_rot = 0, col=col_fun,top_annotation = ta,heatmap_legend_param = list(title = "Expression: log(TPM)"))
#get the column order
colord<-column_order(HM_all)
## Warning: The heatmap has not been initialized. You might have different results
## if you repeatedly execute this function, e.g. when row_km/column_km was
## set. It is more suggested to do as `ht = draw(ht); column_order(ht)`.
colord<-colnames(filt_mat)[colord]
draw(HM_all)
pdf(file="../results/big_heatmap_unseparated.pdf",width=6,height=6)
draw(HM_all)
dev.off()
## quartz_off_screen
## 2
#define function
draw_heatmap_by_group<-function(gene_group,annotation_table = annotation_temp,matrix = trans_mat, order = colord){
list<-annotation_table$TranscriptID[annotation_table$Function==gene_group]
filt_mat<-subset(matrix, rownames(matrix) %in% list)
HM = Heatmap(filt_mat, show_row_names = F, show_column_names = T, row_title = gene_group, row_title_rot = 0, col=col_fun, show_heatmap_legend = FALSE,
cluster_columns = FALSE,column_order = order,
column_names_gp = gpar(fontsize = 6, font="Arial"),
row_title_gp = gpar(fontsize = 7, font="Arial"))
return(HM)
}
#make a list of all gene groups in the right order
annotation_temp<-annotation %>% left_join(mult_list %>% select(Function, Function_type) %>% unique()) %>% arrange(Function)
annotation_temp$Function_type<-factor(annotation_temp$Function_type,
levels=c("Fungal multicellularity", "Expression regulation","Signal transduction"),ordered = T)
annotation_temp<-annotation_temp %>% arrange(Function_type)
#rename some of the functions to make shorter
annotation_temp$Function[annotation_temp$Function=="Acetyl-CoA production and metabolism"]<-"Acetyl-CoA production\nand metabolism"
annotation_temp$Function[annotation_temp$Function=="Cell division, proliferation and growth"]<-"Cell division and growth"
annotation_temp$Function[annotation_temp$Function=="Cell surface and cell wall proteins"]<-"Cell wall proteins"
annotation_temp$Function[annotation_temp$Function=="Cell surface and cell wall proteins"]<-"Cell wall proteins"
#apply to all gene groups
l<-lapply(as.vector(unique(annotation_temp$Function)),draw_heatmap_by_group)
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
#add other gene groups, which aren't in the multicellularity list
#protein kinases
kinase_list<-funannot$TranscriptID[grepl("IPR000719",funannot$InterPro_new) & funannot$TranscriptID %in% sig$target_id[sig$change %in% c("lichen","culture")]]
filt_mat_kinase<-subset(trans_mat, rownames(trans_mat) %in% kinase_list)
HM_kinase = Heatmap(filt_mat_kinase, show_row_names = F, show_column_names = T, row_title = "Protein Kinases", row_title_rot = 0, col=col_fun, show_heatmap_legend = FALSE,
cluster_columns = FALSE,column_order = colord,
column_names_gp = gpar(fontsize = 6, font="Arial"),
row_title_gp = gpar(fontsize = 7, font="Arial"))
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
#NLRs
nlr_list<-nlr_sig$target_id[nlr_sig$change %in% c("lichen","culture")]
filt_mat_nlr<-subset(trans_mat, rownames(trans_mat) %in% nlr_list)
HM_nlr = Heatmap(filt_mat_nlr, show_row_names = F, show_column_names = T, row_title = "Putative NLRs", row_title_rot = 0, col=col_fun, show_heatmap_legend = FALSE,
cluster_columns = FALSE,column_order = colord,
column_names_gp = gpar(fontsize = 6, font="Arial"),
row_title_gp = gpar(fontsize = 7, font="Arial"))
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
#Other het-incopatibility
het_list<-het_sig$TranscriptID[het_sig$change %in% c("lichen","culture") & !(het_sig$TranscriptID %in% nlr_list)]
filt_mat_het<-subset(trans_mat, rownames(trans_mat) %in% het_list)
HM_het = Heatmap(filt_mat_het, show_row_names = F, show_column_names = T, row_title = "Other self/non-self\nrecognition", row_title_rot = 0, col=col_fun, show_heatmap_legend = FALSE,
cluster_columns = FALSE,column_order = colord,
column_names_gp = gpar(fontsize = 6, font="Arial"),
row_title_gp = gpar(fontsize = 7, font="Arial"))
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
#replace 4 panels for signaling pathways with one
signaling_list<-annotation$TranscriptID[annotation$Function %in% c("G-proteins and GPCR", "MAPK signaling pathway","Oxylipins","Velvet")]
filt_mat_signal<-subset(trans_mat, rownames(trans_mat) %in% signaling_list)
HM_signal = Heatmap(filt_mat_signal, show_row_names = F, show_column_names = T, row_title = "Signal transduction", row_title_rot = 0, col=col_fun, show_heatmap_legend = FALSE,
cluster_columns = FALSE,column_order = colord,
column_names_gp = gpar(fontsize = 6, font="Arial"),
row_title_gp = gpar(fontsize = 7, font="Arial"))
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
#draw
ht_list <- l[[4]] %v% l[[5]] %v% l[[7]] %v% l[[6]] %v% l[[3]] %v% l[[8]] %v%
l[[20]] %v% l[[14]] %v% l[[1]] %v% l[[11]] %v% l[[2]] %v% l[[15]] %v% l[[16]] %v% l[[19]] %v% HM_signal %v% HM_kinase %v% HM_nlr %v% HM_het
#draw in two parts
ht_list1 <- l[[4]] %v% l[[5]] %v% l[[7]] %v% l[[6]] %v% l[[3]] %v% l[[8]] %v%
l[[20]] %v% l[[14]] %v% l[[1]] %v% l[[11]] %v% l[[2]]
ht_list2 <- l[[15]] %v% l[[16]] %v% l[[19]] %v% HM_signal %v% HM_kinase %v% HM_nlr %v% HM_het
draw(ht_list1)
pdf(file="../results/big_heatmap_part1.pdf",width=4.25,height=4.5)
draw(ht_list1, newpage = FALSE)
dev.off()
## quartz_off_screen
## 2
pdf(file="../results/big_heatmap_part2.pdf",width=4,height=3.5)
draw(ht_list2)
dev.off()
## quartz_off_screen
## 2
parietin_list<-c("XANPAGTX0501_008850-T1","XANPAGTX0501_008851-T1","XANPAGTX0501_008852-T1","XANPAGTX0501_008853-T1")
filt_mat_parietin<-subset(trans_mat, rownames(trans_mat) %in% parietin_list)
HM_parietin = Heatmap(filt_mat_parietin, show_row_names = T, show_column_names = T,cluster_rows = FALSE, row_title_rot = 0, col=viridis(100), heatmap_legend_param = list(title = "Expression: log(TPM)"), top_annotation = ta)
pdf(file="../results/parietin_heatmap.pdf",width=10,height=2.5)
draw(HM_parietin)
dev.off()
## quartz_off_screen
## 2
HM_parietin
secreted_list<-secreted_sig$target_id[secreted_sig$change!="low_logFC"]
filt_mat_secreted<-subset(trans_mat, rownames(trans_mat) %in% secreted_list)
HM_secreted = Heatmap(filt_mat_secreted, show_row_names = F, show_column_names = T,cluster_rows = T, row_title_rot = 0, col=viridis(100), heatmap_legend_param = list(title = "Expression: log(TPM)"), top_annotation = ta)
pdf(file="../results/secreted_dge_heatmap.pdf",width=10,height=8)
draw(HM_secreted)
dev.off()
## quartz_off_screen
## 2
HM_secreted
plot_bootstrap(so,
target_id = "XANPAGTX0501_009887-T1",
units = "est_counts",
color_by = "condition")
* Make heat map for the same effector
filt_mat_eff<-subset(trans_mat, rownames(trans_mat) =="XANPAGTX0501_009887-T1")
HM_eff = Heatmap(filt_mat_eff, show_row_names = F, show_column_names = T,cluster_rows = T, row_title_rot = 0, col=viridis(100), heatmap_legend_param = list(title = "Expression: log(TPM)"), top_annotation = ta)
pdf(file="../results/XANPAGTX0501_009887-T1_heatmap.pdf",width=10,height=2)
draw(HM_eff)
dev.off()
## quartz_off_screen
## 2
HM_eff
antismash_core<-antismash_gene_all %>% filter(Core_gene==T) %>%
left_join(funannot2,relationship = "many-to-many") %>%
left_join(sig, by = c("TranscriptID"="target_id"))
filt_mat_core<-subset(trans_mat, rownames(trans_mat) %in% antismash_core$TranscriptID)
#define row annotation
##for one protein, XANPAGTX0501_001694-T1, we had two annotations since it is a core gene in two cluster: Xp_GTX0501_2_Cluster_6 and Xp_GTX0501_2_Cluster_7. here I picked Xp_GTX0501_2_Cluster_7, since Xp_GTX0501_2_Cluster_6 had two core genes
ra<-data.frame("TranscriptID"=rownames(filt_mat_core)) %>% left_join(antismash_core) %>%
filter(TranscriptID!="XANPAGTX0501_001694-T1"|Cluster!="Xp_GTX0501_2_Cluster_6") %>%
select(Description)
ra_colors = c("fungal-RiPP-like"= brewer.pal(8,"Dark2")[1], "NRP-metallophore"= brewer.pal(8,"Dark2")[4], "NRPS"= brewer.pal(8,"Dark2")[3],
"NRPS-like"= brewer.pal(8,"Dark2")[5], "NRPS,T1PKS"= brewer.pal(8,"Dark2")[7], "T1PKS"= brewer.pal(8,"Dark2")[6],
"T3PKS" = brewer.pal(8,"Dark2")[8], "terpene"= brewer.pal(8,"Dark2")[2])
ra = rowAnnotation(df = ra,col = list(Description = ra_colors))
HM_core = Heatmap(filt_mat_core, show_row_names = F, show_column_names = T,
row_title_rot = 0, col=col_fun, show_heatmap_legend = FALSE,
cluster_columns = FALSE,column_order = colord,
column_names_gp = gpar(fontsize = 6, font="Arial"),
row_title_gp = gpar(fontsize = 7, font="Arial"),
top_annotation = ta,
right_annotation = ra)
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
pdf(file="../results/all_core_SM_heatmap.pdf",width=8,height=8)
draw(HM_core)
dev.off()
## quartz_off_screen
## 2
#get order of the rows in the heatmap and match to b values
rord = row_order(HM_core)
## Warning: The heatmap has not been initialized. You might have different results
## if you repeatedly execute this function, e.g. when row_km/column_km was
## set. It is more suggested to do as `ht = draw(ht); row_order(ht)`.
rord<-rownames(filt_mat_core)[rord]
core_dge<-data.frame("TranscriptID"=rord) %>% left_join(antismash_core) %>%
filter(TranscriptID!="XANPAGTX0501_001694-T1"|Cluster!="Xp_GTX0501_2_Cluster_6") %>%
select(TranscriptID,b,Description)
head(core_dge)
## TranscriptID b Description
## 1 XANPAGTX0501_001972-T1 2.363522 NRPS
## 2 XANPAGTX0501_001973-T1 2.358272 T1PKS
## 3 XANPAGTX0501_009715-T1 2.760824 fungal-RiPP-like
## 4 XANPAGTX0501_009716-T1 2.958263 fungal-RiPP-like
## 5 XANPAGTX0501_009866-T1 NA terpene
## 6 XANPAGTX0501_001064-T1 -1.531609 fungal-RiPP-like
cl_int<-read.delim2("../../10_lichen_effectors/analysis_and_temp_files/05_cluster_structures/clustering_results.txt") %>% filter(ClusterID %in% c("cl04","cl16","cl18","cl19","cl20","cl21","cl22","cl23",
"cl24","cl24a","cl37","cl38","cl40","cl41","cl42","cl80",
"cl29","cl34"),Gene_Expression!="Non-DGE")
filt_mat_int<-subset(trans_mat, rownames(trans_mat) %in% cl_int$ProteinID)
#define row annotation
ra2<-data.frame("ProteinID"=rownames(filt_mat_int)) %>% left_join(cl_int) %>%
select(ClusterID)
#define color to match the tree
col_cl<-read.delim2("../../10_lichen_effectors/analysis_and_temp_files/05_cluster_structures/cluster_col.txt",sep=",") %>% filter(cluster_id %in% cl_int$ClusterID)
ra2_colors<-as.character(col_cl$color)
names(ra2_colors)<-as.character(col_cl$cluster_id)
ra2 = rowAnnotation(df = ra2,col = list(ClusterID = ra2_colors),show_legend = F)
ta2 = HeatmapAnnotation(df=s2c,col = list(condition = ta_colors),show_legend = F)
HM_int = Heatmap(filt_mat_int, show_row_names = T, show_column_names = T,
row_title_rot = 0, col=col_fun, show_heatmap_legend = F,
cluster_columns = FALSE,column_order = colord,
top_annotation = ta2,
right_annotation = ra2,
column_names_gp = gpar(fontsize = 6),
row_names_gp = gpar(fontsize = 6))
pdf(file="../results/all_secretome_int_heatmap.pdf",width=4,height=4)
draw(HM_int)
dev.off()
## quartz_off_screen
## 2
#get order of rows to match to clusters
rord = row_order(HM_int)
## Warning: The heatmap has not been initialized. You might have different results
## if you repeatedly execute this function, e.g. when row_km/column_km was
## set. It is more suggested to do as `ht = draw(ht); row_order(ht)`.
rord<-rownames(filt_mat_int)[rord]
rord2<-data.frame("ProteinID"=rord) %>% left_join(cl_int)
#get number of DGE per cluster of interest
t<-read.delim2("../../10_lichen_effectors/analysis_and_temp_files/05_cluster_structures/clustering_results.txt") %>% filter(ClusterID %in% c("cl04","cl16","cl18","cl19","cl20","cl21","cl22","cl23",
"cl24","cl24a","cl37","cl38","cl40","cl41","cl42","cl80",
"cl29","cl34"))
t%>% group_by(ClusterID,Gene_Expression) %>% summarise(n=n()) %>%
pivot_wider(names_from = Gene_Expression,values_from = n,values_fill=0)
## # A tibble: 18 × 3
## # Groups: ClusterID [18]
## ClusterID `Non-DGE` `Upregulated in lichen`
## <chr> <int> <int>
## 1 cl04 6 2
## 2 cl16 2 0
## 3 cl18 2 4
## 4 cl19 3 1
## 5 cl20 7 0
## 6 cl21 4 1
## 7 cl22 0 2
## 8 cl23 2 1
## 9 cl24 5 4
## 10 cl24a 6 5
## 11 cl29 3 1
## 12 cl34 3 1
## 13 cl37 1 1
## 14 cl38 3 1
## 15 cl40 1 1
## 16 cl41 0 3
## 17 cl42 0 1
## 18 cl80 1 1